15 Milo: Differential Abundance
Changes in gene expression are only part of the story. In many studies, the more important biological signal is that certain cell states become more or less abundant across conditions, donors, or time points.
sclet provides a state-aware interface to miloR for cell neighbourhood differential abundance (DA) analysis.
The Milo functionality in sclet is an optional dependency: you need to install miloR to run the examples. In the GitHub Actions bookdown workflow, these chunks are executed when the required packages are available, so this chapter also acts as a regression check for the DA integration layer.
15.1 Requirements
Before running Milo DA, prepare a SingleCellExperiment with:
reducedDims(sce)$PCAcolData(sce)containing a sample column and a condition column
UMAP is optional (used for visualization only).
15.2 Two-group DA (GLM)
colData(sce)$Sample <- paste(colData(sce)$SortDay, colData(sce)$Age, sep = "_")
sce <- NormalizeData(sce)
sce <- RunPCA(sce)
sce <- RunUMAP(sce)
res <- RunMilo(
sce = sce,
sample_col = "Sample",
condition_col = "Age",
name = "milo_main",
contrasts = c("Age1wk - Age4wk"),
k1 = 11, k2 = 11, d1 = 40, d2 = 40, prop = 0.2
)
da <- res$da_results
table(da$SpatialFDR < 0.1)##
## FALSE
## 343## logFC logCPM F PValue FDR Nhood
## 1 -0.4248810 13.66075 0.12423442 0.72449737 1.0000000 1
## 2 -1.1178226 13.37924 0.71801065 0.39682679 0.7519977 2
## 3 0.3680766 13.57295 0.08235778 0.77413595 1.0000000 3
## 4 -2.8623635 13.87550 4.13557017 0.04202933 0.2640309 4
## 5 -2.8294618 13.65808 4.27942341 0.03861381 0.2508434 5
## 6 -1.4177180 13.55053 1.21268563 0.27083953 0.6156011 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 1.0000000 Age1wk - Age4wk 0.72449737
## 2 0.7573074 Age1wk - Age4wk 0.39682679
## 3 1.0000000 Age1wk - Age4wk 0.77413595
## 4 0.2898203 Age1wk - Age4wk 0.04202933
## 5 0.2714430 Age1wk - Age4wk 0.03861381
## 6 0.6258870 Age1wk - Age4wk 0.27083953## $id
## [1] "milo_main"
##
## $type
## [1] "milo"
##
## $status
## [1] "completed"
##
## $method
## [1] "miloR"
##
## $inputs
## $inputs$reduction
## [1] "PCA"
##
## $inputs$sample_col
## [1] "Sample"
##
## $inputs$condition_col
## [1] "Age"
##
## $inputs$covariates
## NULL
##
##
## $artifacts
## $artifacts$analysis_key
## [1] "milo"
##
## $artifacts$da_results
## logFC logCPM F PValue
## 1 -0.424880954 13.66075 1.242344e-01 0.7244973681
## 2 -1.117822619 13.37924 7.180106e-01 0.3968267906
## 3 0.368076626 13.57295 8.235778e-02 0.7741359491
## 4 -2.862363545 13.87550 4.135570e+00 0.0420293274
## 5 -2.829461820 13.65808 4.279423e+00 0.0386138100
## 6 -1.417717985 13.55053 1.212686e+00 0.2708395280
## 7 2.411644567 13.35979 3.431824e+00 0.0639943505
## 8 -1.528117211 13.49564 1.496937e+00 0.2211852757
## 9 -0.004906545 13.40558 3.366998e-05 0.9953704028
## 10 -3.980828065 13.38533 7.484133e+00 0.0062405123
## 11 -0.176192860 13.60726 1.845353e-02 0.8919487757
## 12 -1.473387179 13.39248 1.227972e+00 0.2678406963
## 13 -2.864754953 13.43724 4.330685e+00 0.0374681945
## 14 -0.665538997 13.55753 3.147359e-01 0.5748068106
## 15 -0.325235904 13.75332 8.294807e-02 0.7733500363
## 16 -1.204195394 13.64289 1.184139e+00 0.2765532447
## 17 -0.015332105 13.41399 1.214456e-04 0.9912076227
## 18 0.000000000 13.52487 0.000000e+00 1.0000000000
## 19 1.251604656 13.54059 1.141458e+00 0.2853819816
## 20 2.759813107 13.47791 4.429930e+00 0.0353502325
## 21 2.070528473 13.65160 2.930971e+00 0.0869404181
## 22 -2.579254060 13.39941 3.761596e+00 0.0524834302
## 23 -0.466985007 13.33484 1.312698e-01 0.7171302338
## 24 3.522365090 13.45113 6.494436e+00 0.0108428632
## 25 -1.772402042 13.71854 1.865492e+00 0.1720370671
## 26 -3.721712027 13.71345 6.797619e+00 0.0091477149
## 27 0.169448871 13.36126 1.342907e-02 0.9780272498
## 28 0.623537211 13.56022 2.695635e-01 0.6036414471
## 29 -0.032617153 13.43381 8.517471e-04 0.9767181269
## 30 0.441833833 13.52357 1.630629e-01 0.6863646865
## 31 -0.891295529 13.77306 5.564567e-01 0.4557169773
## 32 -1.482867854 13.65031 1.310430e+00 0.2523568330
## 33 0.253254184 13.99112 4.509472e-02 0.8318362578
## 34 0.761754415 13.34543 3.666721e-01 0.5448439125
## 35 -0.844614803 13.60263 4.263750e-01 0.5137949331
## 36 0.000000000 13.63346 0.000000e+00 1.0000000000
## 37 -2.574031743 13.61366 3.650923e+00 0.0560797826
## 38 0.744413041 13.42664 3.230858e-01 0.5697776543
## 39 -1.185717566 13.47918 1.220120e+00 0.2693758914
## 40 0.916331256 13.82054 6.419369e-01 0.4230380362
## 41 -0.251978393 13.54110 4.302831e-02 0.8356781395
## 42 -0.223363849 13.60682 3.314110e-02 0.8555512418
## 43 -0.057057273 13.46196 1.914739e-03 0.9780272575
## 44 0.518061348 13.38562 1.648353e-01 0.6847558982
## 45 -2.258750850 13.71189 3.091563e+00 0.0787437793
## 46 -1.838154533 13.36053 2.330569e+00 0.1269016175
## 47 0.000000000 13.52870 0.000000e+00 1.0000000000
## 48 -1.188698301 13.60336 1.181955e+00 0.2769966488
## 49 0.000000000 13.77713 0.000000e+00 1.0000000000
## 50 -1.185802257 13.48131 1.220819e+00 0.2692388196
## 51 0.373582963 13.81322 1.080639e-01 0.7423692419
## 52 -2.836136439 13.47682 4.313801e+00 0.0378415327
## 53 -1.246600777 13.55548 9.774095e-01 0.3228740661
## 54 1.238345509 13.59173 1.424484e+00 0.2327080509
## 55 1.071904932 13.52451 8.108193e-01 0.3679097488
## 56 0.122787309 13.38286 9.275920e-03 0.9835147909
## 57 -1.202367177 13.46901 1.230838e+00 0.2678944184
## 58 0.381292023 13.50587 9.745086e-02 0.7549199073
## 59 1.267997488 13.48212 1.000227e+00 0.3172909656
## 60 -0.681563634 13.82784 2.493612e-01 0.6175412149
## 61 0.098821777 13.37891 6.709147e-03 0.9347211625
## 62 0.000000000 13.36367 0.000000e+00 1.0000000000
## 63 -2.512702862 13.63493 3.318322e+00 0.0685552560
## 64 -1.201211763 13.38506 1.273519e+00 0.2678944184
## 65 -4.076428534 13.72174 7.893261e+00 0.0049759791
## 66 0.000000000 13.40962 0.000000e+00 1.0000000000
## 67 0.019982643 13.74482 2.888134e-04 0.9864414893
## 68 -3.751840144 13.53703 7.011996e+00 0.0081150618
## 69 -3.068945742 13.42384 4.871700e+00 0.0273335816
## 70 1.180128789 13.40490 8.257773e-01 0.3635283273
## 71 -1.189703306 13.71189 1.167362e+00 0.2799818373
## 72 3.214770613 13.38068 5.521875e+00 0.0188082991
## 73 0.000000000 13.91102 0.000000e+00 1.0000000000
## 74 -1.357412247 13.42397 9.793027e-01 0.3224059266
## 75 0.000000000 13.31744 0.000000e+00 1.0000000000
## 76 -4.050595281 13.92972 7.369754e+00 0.0066495952
## 77 0.000000000 13.45196 0.000000e+00 1.0000000000
## 78 0.350342673 13.43104 8.689270e-02 0.7681741709
## 79 -0.222803764 13.75660 3.938317e-02 0.8426973727
## 80 -3.145858560 13.54091 5.222271e+00 0.0223297923
## 81 -2.482608170 13.44524 3.350681e+00 0.0672205614
## 82 -1.204292534 13.66093 1.184224e+00 0.2765359354
## 83 0.000000000 13.44745 0.000000e+00 1.0000000000
## 84 -1.688098824 13.76266 1.701559e+00 0.1921279246
## 85 -3.703001112 13.51270 6.864023e+00 0.0088142054
## 86 0.000000000 13.49337 0.000000e+00 1.0000000000
## 87 -1.798180840 13.50322 2.198649e+00 0.1381776906
## 88 -2.242607368 13.45573 2.972439e+00 0.0847391255
## 89 0.125948815 13.39763 1.009465e-02 0.9505375356
## 90 0.000000000 13.51051 0.000000e+00 1.0000000000
## 91 1.689734201 13.90862 2.057984e+00 0.1514559101
## 92 0.531750415 13.53974 2.036327e-01 0.6518187452
## 93 1.392989067 13.50140 1.336013e+00 0.2477785104
## 94 -0.425620309 13.40358 8.643441e-02 0.7687688689
## 95 2.911714110 13.49798 5.019058e+00 0.0251016854
## 96 -0.103310636 13.51971 7.253509e-03 0.9321306865
## 97 4.645694875 13.41742 1.044808e+01 0.0012335734
## 98 2.276735586 13.48771 3.185481e+00 0.0743393180
## 99 -3.896827775 13.77632 7.154646e+00 0.0074947403
## 100 0.000000000 13.57378 0.000000e+00 1.0000000000
## 101 2.491426644 13.40460 3.521474e+00 0.0606209534
## 102 0.000000000 13.36593 0.000000e+00 1.0000000000
## 103 0.000000000 13.38795 0.000000e+00 1.0000000000
## 104 -1.429238917 13.74524 1.420977e+00 0.2332839513
## 105 0.000000000 13.50619 0.000000e+00 1.0000000000
## 106 -0.888319018 13.40719 4.502326e-01 0.5022470897
## 107 0.526410077 13.45027 1.797379e-01 0.6716119050
## 108 -2.188586199 13.52521 2.650146e+00 0.1035862918
## 109 -3.272433596 13.42831 5.256968e+00 0.0218891903
## 110 -3.744580182 13.42334 6.708405e+00 0.0096162420
## 111 -0.201206321 13.52823 2.425454e-02 0.8762435723
## 112 0.050160184 13.42569 3.295395e-03 0.9542238290
## 113 -0.883005823 13.61723 5.255705e-01 0.4684998110
## 114 -0.693284835 13.54719 3.044082e-01 0.5811499827
## 115 0.000000000 13.58075 0.000000e+00 1.0000000000
## 116 -0.223380264 13.49849 2.900204e-02 0.8647793384
## 117 0.000000000 13.40962 0.000000e+00 1.0000000000
## 118 -1.533255109 13.38229 1.294709e+00 0.2552217491
## 119 3.377092321 13.41682 6.023178e+00 0.0141438691
## 120 -1.193437091 13.72690 8.496784e-01 0.3566757461
## 121 -1.124099327 13.32192 7.625266e-01 0.3825695460
## 122 1.384943428 13.69011 1.370943e+00 0.2416906375
## 123 -0.828401318 13.50617 4.043823e-01 0.5248559278
## 124 -1.524385781 13.48467 1.377668e+00 0.2405395627
## 125 -1.472351651 13.52659 1.388312e+00 0.2387311787
## 126 0.000000000 13.99179 0.000000e+00 1.0000000000
## 127 2.629388104 13.45333 3.905975e+00 0.0481546893
## 128 3.915311769 13.56029 8.560569e+00 0.0034464866
## 129 -2.560054117 13.41227 3.705500e+00 0.0542747207
## 130 -3.438458368 13.73183 5.930068e+00 0.0149099714
## 131 -3.077919719 13.47893 4.773743e+00 0.0289306568
## 132 0.000000000 13.64616 0.000000e+00 1.0000000000
## 133 0.950328974 13.47432 5.979007e-01 0.4394067523
## 134 0.098538182 13.37656 6.685164e-03 0.9348376806
## 135 0.000000000 13.97159 0.000000e+00 1.0000000000
## 136 -1.324802122 13.53687 1.128667e+00 0.2880973078
## 137 -1.188718567 13.60745 1.179203e+00 0.2775565213
## 138 -1.186914885 13.51157 1.235116e+00 0.2678944176
## 139 -2.240457134 13.53597 3.034627e+00 0.0815501153
## 140 0.621646147 13.42053 2.428474e-01 0.6221728371
## 141 0.906703741 13.44685 4.227834e-01 0.5155731990
## 142 -2.595803093 13.53630 3.810811e+00 0.0509634212
## 143 -2.212850425 13.57491 2.636473e+00 0.1044811113
## 144 -1.189643431 13.70679 1.168879e+00 0.2796696834
## 145 -2.254301116 13.67604 2.958472e+00 0.0854737563
## 146 -0.399918474 13.77278 1.233487e-01 0.7254413918
## 147 0.381848164 13.71829 1.092489e-01 0.7410109769
## 148 -4.293656540 13.59428 8.650664e+00 0.0032803505
## 149 -1.171432575 13.37771 1.257888e+00 0.2678944172
## 150 0.002114379 13.74663 2.587379e-06 0.9987166236
## 151 -2.226398894 13.43367 2.955089e+00 0.0856526837
## 152 -1.209450348 13.32701 8.735057e-01 0.3500195087
## 153 3.565903263 13.46420 6.654877e+00 0.0099090918
## 154 0.000000000 13.45140 0.000000e+00 1.0000000000
## 155 0.000000000 13.66416 0.000000e+00 1.0000000000
## 156 0.362978077 13.54463 9.764261e-02 0.7546866450
## 157 3.886316627 13.61152 8.264505e+00 0.0040552053
## 158 -1.766103700 13.52619 1.828883e+00 0.1763041664
## 159 -0.501424028 13.44845 1.616602e-01 0.6876450759
## 160 -0.087440139 13.48441 6.541658e-03 0.9355393360
## 161 0.000000000 13.86004 0.000000e+00 1.0000000000
## 162 -1.202948077 13.53331 1.235690e+00 0.2678944183
## 163 0.126028336 13.70955 1.164433e-02 0.9140711029
## 164 -1.192014580 13.53860 9.281189e-01 0.3353861575
## 165 -1.502425869 13.45352 1.208040e+00 0.2717592080
## 166 -0.167468828 13.44055 1.763621e-02 0.8943543371
## 167 -1.628967656 13.34295 1.474342e+00 0.2247036814
## 168 -0.005158776 13.43394 6.185418e-04 0.9801589808
## 169 0.000000000 13.60817 0.000000e+00 1.0000000000
## 170 0.847656077 13.45467 4.587363e-01 0.4982380164
## 171 -2.235746397 13.61874 2.921969e+00 0.0874264151
## 172 -4.519928792 13.45216 9.125479e+00 0.0025300269
## 173 2.534663268 13.52782 4.092716e+00 0.0431070809
## 174 0.000000000 13.61327 0.000000e+00 1.0000000000
## 175 3.356959879 13.65586 6.710986e+00 0.0096023485
## 176 -1.821585953 13.95295 1.951183e+00 0.1625045704
## 177 -0.879703102 13.35995 4.520269e-01 0.5013966180
## 178 4.789226849 13.45815 1.105753e+01 0.0008879162
## 179 -4.596204439 13.50774 9.847491e+00 0.0017078414
## 180 0.121679352 13.61037 1.157044e-02 0.9143431418
## 181 -1.201051210 13.33962 1.335467e+00 0.2678944184
## 182 -3.603619302 13.39472 6.268238e+00 0.0123151771
## 183 -0.294809578 13.50575 5.634568e-02 0.8123749416
## 184 -1.162697830 13.37973 8.025269e-01 0.3703703880
## 185 0.000000000 13.81226 0.000000e+00 1.0000000000
## 186 -0.971714712 13.53391 5.943255e-01 0.4407778678
## 187 -0.684553806 13.63758 3.057935e-01 0.5802910091
## 188 0.000000000 13.68603 0.000000e+00 1.0000000000
## 189 1.130379002 13.50436 8.718035e-01 0.3504893744
## 190 -0.272197146 13.63700 4.301713e-02 0.8356991819
## 191 -2.240781558 13.54103 3.034951e+00 0.0815338398
## 192 1.367062279 13.55996 1.341174e+00 0.2468673438
## 193 -0.275028185 13.45096 4.246819e-02 0.8367360063
## 194 1.371160152 13.70081 1.509263e+00 0.2192937441
## 195 -1.184995847 13.39601 7.734980e-01 0.3791679049
## 196 -1.918463089 13.62171 1.938475e+00 0.1638792936
## 197 0.000000000 13.51508 0.000000e+00 1.0000000000
## 198 -2.860601683 13.50740 4.462162e+00 0.0346896585
## 199 0.000000000 13.51397 0.000000e+00 1.0000000000
## 200 0.995836034 13.50286 6.735245e-01 0.4118540236
## 201 -1.004547699 13.55005 6.837056e-01 0.4083423957
## 202 1.884987801 13.51184 2.336406e+00 0.1264269397
## 203 1.023058942 13.76308 8.113541e-01 0.3677518407
## 204 3.464091303 13.45266 6.158488e+00 0.0131020605
## 205 0.000000000 13.74156 0.000000e+00 1.0000000000
## 206 -0.882980583 13.59076 4.654024e-01 0.4951329656
## 207 -1.402994531 13.49527 1.213124e+00 0.2707529850
## 208 1.978626874 13.46933 2.368934e+00 0.1238176360
## 209 0.967442992 13.77281 7.074300e-01 0.4003276345
## 210 -0.477408152 13.62649 1.578501e-01 0.6911559990
## 211 2.338989984 13.55734 3.275232e+00 0.0703767388
## 212 0.246223681 13.47759 4.032034e-02 0.8408614922
## 213 0.203306790 13.65588 2.853049e-02 0.8658726458
## 214 -3.095781503 13.38677 4.996528e+00 0.0254302673
## 215 -2.604552041 13.68583 3.717569e+00 0.0538839436
## 216 -1.288113019 13.64621 1.057889e+00 0.3037334699
## 217 -1.917488676 13.45381 2.019510e+00 0.1553346859
## 218 0.170826650 13.87011 2.274403e-02 0.8801290437
## 219 -2.227788316 13.45941 2.954295e+00 0.0856947784
## 220 -1.998653948 13.40175 2.233177e+00 0.1351218277
## 221 -1.262350106 13.78209 1.172869e+00 0.2788506707
## 222 -0.418667127 13.40831 1.051099e-01 0.7457915157
## 223 0.000000000 13.64325 0.000000e+00 1.0000000000
## 224 0.000000000 13.38399 0.000000e+00 1.0000000000
## 225 0.000000000 13.68194 0.000000e+00 1.0000000000
## 226 2.540943709 13.43549 3.628218e+00 0.0568493799
## 227 0.030120426 13.51820 2.286221e-03 0.9618655201
## 228 -1.804226187 13.45374 2.161012e+00 0.1415972887
## 229 0.000000000 13.41787 0.000000e+00 1.0000000000
## 230 0.089685702 13.45690 5.660558e-03 0.9400285969
## 231 -1.883063680 13.33688 1.981282e+00 0.1593006943
## 232 -2.488295910 13.54323 3.703201e+00 0.0543494965
## 233 -1.202093576 13.44827 1.226578e+00 0.2681124255
## 234 0.000000000 13.75786 0.000000e+00 1.0000000000
## 235 -2.555632030 13.44727 3.633433e+00 0.0566716255
## 236 -0.439113494 13.58434 1.389179e-01 0.7093706698
## 237 1.994304500 13.51333 2.650205e+00 0.1035824867
## 238 -0.690441808 13.57915 3.075520e-01 0.5792043308
## 239 0.916396683 13.72871 6.424639e-01 0.4228477645
## 240 0.298424457 13.41960 4.491505e-02 0.8321666153
## 241 -0.518479256 13.43662 1.681829e-01 0.6817446313
## 242 -4.605680901 13.75034 9.887286e+00 0.0016713512
## 243 0.000000000 13.78072 0.000000e+00 1.0000000000
## 244 0.000000000 13.36415 0.000000e+00 1.0000000000
## 245 -2.856727901 13.63482 4.313260e+00 0.0378535621
## 246 0.000000000 13.47492 0.000000e+00 1.0000000000
## 247 -3.436700504 13.67958 5.810328e+00 0.0159584625
## 248 5.164141698 13.56788 1.308519e+01 0.0002997796
## 249 -2.274918162 13.42886 3.038436e+00 0.0813590526
## 250 0.372717041 13.40032 8.789145e-02 0.7668840292
## 251 0.000000000 13.47219 0.000000e+00 1.0000000000
## 252 -1.839919711 13.44875 2.204737e+00 0.1376332700
## 253 -0.623790677 13.53936 2.322451e-01 0.6298794729
## 254 -3.245523233 13.33016 5.704720e+00 0.0169462337
## 255 -4.453097346 13.57873 9.392209e+00 0.0021875590
## 256 0.000000000 13.35504 0.000000e+00 1.0000000000
## 257 0.528970590 13.53670 1.985241e-01 0.6559288634
## 258 -1.383505065 13.64084 1.132693e+00 0.2872391837
## 259 -0.541950770 13.79529 2.180863e-01 0.6405167911
## 260 0.000000000 13.56247 0.000000e+00 1.0000000000
## 261 -1.565028125 13.85595 1.421423e+00 0.2332105986
## 262 0.000000000 13.48125 0.000000e+00 1.0000000000
## 263 -1.233077916 13.39357 8.295595e-01 0.3624319322
## 264 -0.167410678 13.64393 2.177882e-02 0.8826813597
## 265 -2.597883443 13.63049 3.688266e+00 0.0548379526
## 266 0.000000000 13.45196 0.000000e+00 1.0000000000
## 267 0.564407210 13.62651 2.354513e-01 0.6275263634
## 268 -2.921220209 13.43771 4.272994e+00 0.0387600615
## 269 -0.403328968 13.59250 1.143704e-01 0.7352326442
## 270 0.857531727 13.40426 4.101410e-01 0.5219193511
## 271 -1.838521101 13.33566 2.395247e+00 0.1217506264
## 272 1.432587820 13.41865 1.313064e+00 0.2518806094
## 273 2.561980921 13.49912 3.664550e+00 0.0556232024
## 274 -1.273003363 13.49613 1.039407e+00 0.3079954004
## 275 -3.040088418 13.60130 4.681882e+00 0.0305167441
## 276 -4.067630206 13.63741 7.868646e+00 0.0050440877
## 277 2.744463519 13.47787 4.325602e+00 0.0375801809
## 278 -2.841470138 13.54390 4.423074e+00 0.0354924259
## 279 0.022954053 13.56449 5.225505e-04 0.9817631196
## 280 -2.263153001 13.40097 3.079140e+00 0.0793470892
## 281 -2.266400521 13.48922 3.055096e+00 0.0805289751
## 282 0.000000000 13.74002 0.000000e+00 1.0000000000
## 283 -4.269673792 13.47778 8.363960e+00 0.0038393892
## 284 -3.064408324 13.43721 4.829270e+00 0.0280137814
## 285 -2.242605199 13.36316 3.120951e+00 0.0773361395
## 286 -1.261074402 13.78086 7.777438e-01 0.3778629412
## 287 0.708080534 13.45800 3.326501e-01 0.5641216667
## 288 0.361743724 13.87130 8.518756e-02 0.7703955531
## 289 0.000000000 13.41102 0.000000e+00 1.0000000000
## 290 -1.549473965 13.80476 1.601658e+00 0.2057113418
## 291 -2.585170487 13.37433 3.816123e+00 0.0508021624
## 292 0.000000000 13.87075 0.000000e+00 1.0000000000
## 293 -1.561259744 13.42378 1.495283e+00 0.2678944522
## 294 1.371522464 13.49454 1.585263e+00 0.2118420747
## 295 -0.204898348 13.47161 2.418030e-02 0.8764315958
## 296 0.516669819 13.73015 1.898415e-01 0.6630622496
## 297 -0.533177853 13.35981 1.677719e-01 0.6821124376
## 298 -2.543913691 13.48659 3.455796e+00 0.0630731786
## 299 0.134526976 13.65110 1.383928e-02 0.9063559887
## 300 -0.605587895 13.32302 2.047466e-01 0.6590283795
## 301 -1.813544231 13.46094 2.177553e+00 0.1400828630
## 302 -1.345893302 13.59251 1.099608e+00 0.2943891056
## 303 -1.203587137 13.62459 1.183788e+00 0.2766243060
## 304 3.213393151 13.66743 5.945418e+00 0.0147807938
## 305 0.393183553 13.45714 1.047357e-01 0.7462288525
## 306 0.797914761 13.42752 4.099718e-01 0.5220052115
## 307 -2.587483646 13.44173 3.691826e+00 0.0547211060
## 308 3.113997446 13.48557 5.156442e+00 0.0231911638
## 309 0.216590758 13.36617 3.052979e-02 0.8612987134
## 310 -2.542200977 13.77976 3.286121e+00 0.0699115942
## 311 -2.585234992 13.77059 3.689281e+00 0.0548046199
## 312 -4.358021041 13.87422 8.523372e+00 0.0035175493
## 313 0.000000000 13.40480 0.000000e+00 1.0000000000
## 314 -2.209603410 13.30578 2.769647e+00 0.0961130385
## 315 0.683767386 13.85598 3.370529e-01 0.5615543744
## 316 0.687328106 13.49532 3.282375e-01 0.5667175268
## 317 -0.690269095 13.50355 3.227912e-01 0.5699536374
## 318 -1.886221206 13.39172 1.819080e+00 0.1774672880
## 319 0.000000000 13.55688 0.000000e+00 1.0000000000
## 320 0.243650930 13.36793 4.187945e-02 0.8378557986
## 321 0.000000000 13.76151 0.000000e+00 1.0000000000
## 322 0.636938385 13.47072 2.338313e-01 0.6287128477
## 323 -3.443484840 13.53760 6.071520e+00 0.0137622123
## 324 0.603441835 13.50057 2.565744e-01 0.6124996870
## 325 -0.070062488 13.65374 4.700496e-03 0.9453417300
## 326 -1.102001219 13.42819 7.210559e-01 0.3958274007
## 327 -1.129900564 13.53967 8.608158e-01 0.3535431364
## 328 -2.264927719 13.45615 3.007621e+00 0.0829187826
## 329 -3.229997791 13.45355 5.266240e+00 0.0217729794
## 330 -0.329393912 13.43705 5.861338e-02 0.8087083603
## 331 -0.380359107 13.37328 9.023108e-02 0.7638926936
## 332 -0.707978650 13.81118 3.655532e-01 0.5454581853
## 333 -0.820495005 13.65112 4.452741e-01 0.5046102345
## 334 3.221109314 13.44767 5.452647e+00 0.0195673894
## 335 -2.099209133 13.61887 2.438011e+00 0.1184724660
## 336 1.730693788 13.44189 1.686980e+00 0.1940431771
## 337 -0.850157785 13.43439 4.436590e-01 0.5053840991
## 338 2.749166600 13.39038 3.948712e+00 0.0469469688
## 339 -1.549258919 13.54426 1.508770e+00 0.2193689719
## 340 2.693552947 13.44685 4.098926e+00 0.0429491365
## 341 -0.255149378 13.43712 4.150790e-02 0.8385667366
## 342 -1.353047618 13.31144 1.057478e+00 0.3038273979
## 343 -0.937536489 13.42697 5.147687e-01 0.4731062196
## FDR Nhood SpatialFDR contrast
## 1 1.0000000 1 1.0000000 Age1wk - Age4wk
## 2 0.7519977 2 0.7573074 Age1wk - Age4wk
## 3 1.0000000 3 1.0000000 Age1wk - Age4wk
## 4 0.2640309 4 0.2898203 Age1wk - Age4wk
## 5 0.2508434 5 0.2714430 Age1wk - Age4wk
## 6 0.6156011 6 0.6258870 Age1wk - Age4wk
## 7 0.2966225 7 0.3169020 Age1wk - Age4wk
## 8 0.6156011 8 0.6258870 Age1wk - Age4wk
## 9 1.0000000 9 1.0000000 Age1wk - Age4wk
## 10 0.1425507 10 0.1436379 Age1wk - Age4wk
## 11 1.0000000 11 1.0000000 Age1wk - Age4wk
## 12 0.6156011 12 0.6258870 Age1wk - Age4wk
## 13 0.2508434 13 0.2714430 Age1wk - Age4wk
## 14 0.9358425 14 0.9553453 Age1wk - Age4wk
## 15 1.0000000 15 1.0000000 Age1wk - Age4wk
## 16 0.6156011 16 0.6258870 Age1wk - Age4wk
## 17 1.0000000 17 1.0000000 Age1wk - Age4wk
## 18 1.0000000 18 1.0000000 Age1wk - Age4wk
## 19 0.6214929 19 0.6344084 Age1wk - Age4wk
## 20 0.2508434 20 0.2714430 Age1wk - Age4wk
## 21 0.3224437 21 0.3344722 Age1wk - Age4wk
## 22 0.2746386 22 0.3013966 Age1wk - Age4wk
## 23 1.0000000 23 1.0000000 Age1wk - Age4wk
## 24 0.1549626 24 0.1717565 Age1wk - Age4wk
## 25 0.5222010 25 0.5288930 Age1wk - Age4wk
## 26 0.1477747 26 0.1615543 Age1wk - Age4wk
## 27 1.0000000 27 1.0000000 Age1wk - Age4wk
## 28 0.9675188 28 0.9903370 Age1wk - Age4wk
## 29 1.0000000 29 1.0000000 Age1wk - Age4wk
## 30 1.0000000 30 1.0000000 Age1wk - Age4wk
## 31 0.8270419 31 0.8479031 Age1wk - Age4wk
## 32 0.6156011 32 0.6258870 Age1wk - Age4wk
## 33 1.0000000 33 1.0000000 Age1wk - Age4wk
## 34 0.9171184 34 0.9342001 Age1wk - Age4wk
## 35 0.8886513 35 0.9050362 Age1wk - Age4wk
## 36 1.0000000 36 1.0000000 Age1wk - Age4wk
## 37 0.2746386 37 0.3013966 Age1wk - Age4wk
## 38 0.9353785 38 0.9539383 Age1wk - Age4wk
## 39 0.6156011 39 0.6258870 Age1wk - Age4wk
## 40 0.7801185 40 0.7954931 Age1wk - Age4wk
## 41 1.0000000 41 1.0000000 Age1wk - Age4wk
## 42 1.0000000 42 1.0000000 Age1wk - Age4wk
## 43 1.0000000 43 1.0000000 Age1wk - Age4wk
## 44 1.0000000 44 1.0000000 Age1wk - Age4wk
## 45 0.3224437 45 0.3329325 Age1wk - Age4wk
## 46 0.4267378 46 0.4364891 Age1wk - Age4wk
## 47 1.0000000 47 1.0000000 Age1wk - Age4wk
## 48 0.6156011 48 0.6258870 Age1wk - Age4wk
## 49 1.0000000 49 1.0000000 Age1wk - Age4wk
## 50 0.6156011 50 0.6258870 Age1wk - Age4wk
## 51 1.0000000 51 1.0000000 Age1wk - Age4wk
## 52 0.2508434 52 0.2714430 Age1wk - Age4wk
## 53 0.6671434 53 0.6789184 Age1wk - Age4wk
## 54 0.6156011 54 0.6258870 Age1wk - Age4wk
## 55 0.7211031 55 0.7359744 Age1wk - Age4wk
## 56 1.0000000 56 1.0000000 Age1wk - Age4wk
## 57 0.6156011 57 0.6258870 Age1wk - Age4wk
## 58 1.0000000 58 1.0000000 Age1wk - Age4wk
## 59 0.6636024 59 0.6759385 Age1wk - Age4wk
## 60 0.9806326 60 1.0000000 Age1wk - Age4wk
## 61 1.0000000 61 1.0000000 Age1wk - Age4wk
## 62 1.0000000 62 1.0000000 Age1wk - Age4wk
## 63 0.3094007 63 0.3326627 Age1wk - Age4wk
## 64 0.6156011 64 0.6258870 Age1wk - Age4wk
## 65 0.1235801 65 0.1288975 Age1wk - Age4wk
## 66 1.0000000 66 1.0000000 Age1wk - Age4wk
## 67 1.0000000 67 1.0000000 Age1wk - Age4wk
## 68 0.1477747 68 0.1615543 Age1wk - Age4wk
## 69 0.2286687 69 0.2351162 Age1wk - Age4wk
## 70 0.7207527 70 0.7317515 Age1wk - Age4wk
## 71 0.6156011 71 0.6258870 Age1wk - Age4wk
## 72 0.1954923 72 0.1997976 Age1wk - Age4wk
## 73 1.0000000 73 1.0000000 Age1wk - Age4wk
## 74 0.6671434 74 0.6789184 Age1wk - Age4wk
## 75 1.0000000 75 1.0000000 Age1wk - Age4wk
## 76 0.1425507 76 0.1493222 Age1wk - Age4wk
## 77 1.0000000 77 1.0000000 Age1wk - Age4wk
## 78 1.0000000 78 1.0000000 Age1wk - Age4wk
## 79 1.0000000 79 1.0000000 Age1wk - Age4wk
## 80 0.2070032 80 0.2129872 Age1wk - Age4wk
## 81 0.3074220 81 0.3284780 Age1wk - Age4wk
## 82 0.6156011 82 0.6258870 Age1wk - Age4wk
## 83 1.0000000 83 1.0000000 Age1wk - Age4wk
## 84 0.5681024 84 0.5741101 Age1wk - Age4wk
## 85 0.1477747 85 0.1615543 Age1wk - Age4wk
## 86 1.0000000 86 1.0000000 Age1wk - Age4wk
## 87 0.4513805 87 0.4598838 Age1wk - Age4wk
## 88 0.3224437 88 0.3329325 Age1wk - Age4wk
## 89 1.0000000 89 1.0000000 Age1wk - Age4wk
## 90 1.0000000 90 1.0000000 Age1wk - Age4wk
## 91 0.4810128 91 0.4914154 Age1wk - Age4wk
## 92 1.0000000 92 1.0000000 Age1wk - Age4wk
## 93 0.6156011 93 0.6258870 Age1wk - Age4wk
## 94 1.0000000 94 1.0000000 Age1wk - Age4wk
## 95 0.2180645 95 0.2259586 Age1wk - Age4wk
## 96 1.0000000 96 1.0000000 Age1wk - Age4wk
## 97 0.1159113 97 0.1036166 Age1wk - Age4wk
## 98 0.3224437 98 0.3329325 Age1wk - Age4wk
## 99 0.1477747 99 0.1615543 Age1wk - Age4wk
## 100 1.0000000 100 1.0000000 Age1wk - Age4wk
## 101 0.2887915 101 0.3169020 Age1wk - Age4wk
## 102 1.0000000 102 1.0000000 Age1wk - Age4wk
## 103 1.0000000 103 1.0000000 Age1wk - Age4wk
## 104 0.6156011 104 0.6258870 Age1wk - Age4wk
## 105 1.0000000 105 1.0000000 Age1wk - Age4wk
## 106 0.8799327 106 0.8945728 Age1wk - Age4wk
## 107 1.0000000 107 1.0000000 Age1wk - Age4wk
## 108 0.3694538 108 0.3808525 Age1wk - Age4wk
## 109 0.2070032 109 0.2129872 Age1wk - Age4wk
## 110 0.1477747 110 0.1615543 Age1wk - Age4wk
## 111 1.0000000 111 1.0000000 Age1wk - Age4wk
## 112 1.0000000 112 1.0000000 Age1wk - Age4wk
## 113 0.8457654 113 0.8681566 Age1wk - Age4wk
## 114 0.9358425 114 0.9566489 Age1wk - Age4wk
## 115 1.0000000 115 1.0000000 Age1wk - Age4wk
## 116 1.0000000 116 1.0000000 Age1wk - Age4wk
## 117 1.0000000 117 1.0000000 Age1wk - Age4wk
## 118 0.6156011 118 0.6258870 Age1wk - Age4wk
## 119 0.1704707 119 0.1852144 Age1wk - Age4wk
## 120 0.7154373 120 0.7306839 Age1wk - Age4wk
## 121 0.7330802 121 0.7399152 Age1wk - Age4wk
## 122 0.6156011 122 0.6258870 Age1wk - Age4wk
## 123 0.8912158 123 0.9057993 Age1wk - Age4wk
## 124 0.6156011 124 0.6258870 Age1wk - Age4wk
## 125 0.6156011 125 0.6258870 Age1wk - Age4wk
## 126 1.0000000 126 1.0000000 Age1wk - Age4wk
## 127 0.2746386 127 0.3013966 Age1wk - Age4wk
## 128 0.1159113 128 0.1200430 Age1wk - Age4wk
## 129 0.2746386 129 0.3013966 Age1wk - Age4wk
## 130 0.1704707 130 0.1865056 Age1wk - Age4wk
## 131 0.2307724 131 0.2399491 Age1wk - Age4wk
## 132 1.0000000 132 1.0000000 Age1wk - Age4wk
## 133 0.8041852 133 0.8222494 Age1wk - Age4wk
## 134 1.0000000 134 1.0000000 Age1wk - Age4wk
## 135 1.0000000 135 1.0000000 Age1wk - Age4wk
## 136 0.6214929 136 0.6344084 Age1wk - Age4wk
## 137 0.6156011 137 0.6258870 Age1wk - Age4wk
## 138 0.6156011 138 0.6258870 Age1wk - Age4wk
## 139 0.3224437 139 0.3329325 Age1wk - Age4wk
## 140 0.9820394 140 1.0000000 Age1wk - Age4wk
## 141 0.8886513 141 0.9050362 Age1wk - Age4wk
## 142 0.2746386 142 0.3013966 Age1wk - Age4wk
## 143 0.3694538 143 0.3808525 Age1wk - Age4wk
## 144 0.6156011 144 0.6258870 Age1wk - Age4wk
## 145 0.3224437 145 0.3329325 Age1wk - Age4wk
## 146 1.0000000 146 1.0000000 Age1wk - Age4wk
## 147 1.0000000 147 1.0000000 Age1wk - Age4wk
## 148 0.1159113 148 0.1200430 Age1wk - Age4wk
## 149 0.6156011 149 0.6258870 Age1wk - Age4wk
## 150 1.0000000 150 1.0000000 Age1wk - Age4wk
## 151 0.3224437 151 0.3329325 Age1wk - Age4wk
## 152 0.7113483 152 0.7222595 Age1wk - Age4wk
## 153 0.1477747 153 0.1615543 Age1wk - Age4wk
## 154 1.0000000 154 1.0000000 Age1wk - Age4wk
## 155 1.0000000 155 1.0000000 Age1wk - Age4wk
## 156 1.0000000 156 1.0000000 Age1wk - Age4wk
## 157 0.1159113 157 0.1204399 Age1wk - Age4wk
## 158 0.5293155 158 0.5362826 Age1wk - Age4wk
## 159 1.0000000 159 1.0000000 Age1wk - Age4wk
## 160 1.0000000 160 1.0000000 Age1wk - Age4wk
## 161 1.0000000 161 1.0000000 Age1wk - Age4wk
## 162 0.6156011 162 0.6258870 Age1wk - Age4wk
## 163 1.0000000 163 1.0000000 Age1wk - Age4wk
## 164 0.6888470 164 0.7004307 Age1wk - Age4wk
## 165 0.6156011 165 0.6258870 Age1wk - Age4wk
## 166 1.0000000 166 1.0000000 Age1wk - Age4wk
## 167 0.6156011 167 0.6258870 Age1wk - Age4wk
## 168 1.0000000 168 1.0000000 Age1wk - Age4wk
## 169 1.0000000 169 1.0000000 Age1wk - Age4wk
## 170 0.8799327 170 0.8945728 Age1wk - Age4wk
## 171 0.3224437 171 0.3344722 Age1wk - Age4wk
## 172 0.1159113 172 0.1046682 Age1wk - Age4wk
## 173 0.2640309 173 0.2898203 Age1wk - Age4wk
## 174 1.0000000 174 1.0000000 Age1wk - Age4wk
## 175 0.1477747 175 0.1615543 Age1wk - Age4wk
## 176 0.5018803 176 0.5068012 Age1wk - Age4wk
## 177 0.8799327 177 0.8945728 Age1wk - Age4wk
## 178 0.1159113 178 0.1036166 Age1wk - Age4wk
## 179 0.1159113 179 0.1036166 Age1wk - Age4wk
## 180 1.0000000 180 1.0000000 Age1wk - Age4wk
## 181 0.6156011 181 0.6258870 Age1wk - Age4wk
## 182 0.1689642 182 0.1844787 Age1wk - Age4wk
## 183 1.0000000 183 1.0000000 Age1wk - Age4wk
## 184 0.7218014 184 0.7362873 Age1wk - Age4wk
## 185 1.0000000 185 1.0000000 Age1wk - Age4wk
## 186 0.8041852 186 0.8222494 Age1wk - Age4wk
## 187 0.9358425 187 0.9566489 Age1wk - Age4wk
## 188 1.0000000 188 1.0000000 Age1wk - Age4wk
## 189 0.7113483 189 0.7222595 Age1wk - Age4wk
## 190 1.0000000 190 1.0000000 Age1wk - Age4wk
## 191 0.3224437 191 0.3329325 Age1wk - Age4wk
## 192 0.6156011 192 0.6258870 Age1wk - Age4wk
## 193 1.0000000 193 1.0000000 Age1wk - Age4wk
## 194 0.6156011 194 0.6258870 Age1wk - Age4wk
## 195 0.7306438 195 0.7399152 Age1wk - Age4wk
## 196 0.5018803 196 0.5073195 Age1wk - Age4wk
## 197 1.0000000 197 1.0000000 Age1wk - Age4wk
## 198 0.2508434 198 0.2714430 Age1wk - Age4wk
## 199 1.0000000 199 1.0000000 Age1wk - Age4wk
## 200 0.7677496 200 0.7784430 Age1wk - Age4wk
## 201 0.7653631 201 0.7743727 Age1wk - Age4wk
## 202 0.4267378 202 0.4364891 Age1wk - Age4wk
## 203 0.7211031 203 0.7359744 Age1wk - Age4wk
## 204 0.1704707 204 0.1852144 Age1wk - Age4wk
## 205 1.0000000 205 1.0000000 Age1wk - Age4wk
## 206 0.8799327 206 0.8945728 Age1wk - Age4wk
## 207 0.6156011 207 0.6258870 Age1wk - Age4wk
## 208 0.4246945 208 0.4349506 Age1wk - Age4wk
## 209 0.7544636 209 0.7625185 Age1wk - Age4wk
## 210 1.0000000 210 1.0000000 Age1wk - Age4wk
## 211 0.3094772 211 0.3329325 Age1wk - Age4wk
## 212 1.0000000 212 1.0000000 Age1wk - Age4wk
## 213 1.0000000 213 1.0000000 Age1wk - Age4wk
## 214 0.2180645 214 0.2259586 Age1wk - Age4wk
## 215 0.2746386 215 0.3013966 Age1wk - Age4wk
## 216 0.6432889 216 0.6564839 Age1wk - Age4wk
## 217 0.4888055 217 0.4977142 Age1wk - Age4wk
## 218 1.0000000 218 1.0000000 Age1wk - Age4wk
## 219 0.3224437 219 0.3329325 Age1wk - Age4wk
## 220 0.4499688 220 0.4598838 Age1wk - Age4wk
## 221 0.6156011 221 0.6258870 Age1wk - Age4wk
## 222 1.0000000 222 1.0000000 Age1wk - Age4wk
## 223 1.0000000 223 1.0000000 Age1wk - Age4wk
## 224 1.0000000 224 1.0000000 Age1wk - Age4wk
## 225 1.0000000 225 1.0000000 Age1wk - Age4wk
## 226 0.2746386 226 0.3013966 Age1wk - Age4wk
## 227 1.0000000 227 1.0000000 Age1wk - Age4wk
## 228 0.4539053 228 0.4613240 Age1wk - Age4wk
## 229 1.0000000 229 1.0000000 Age1wk - Age4wk
## 230 1.0000000 230 1.0000000 Age1wk - Age4wk
## 231 0.4967285 231 0.4993197 Age1wk - Age4wk
## 232 0.2746386 232 0.3013966 Age1wk - Age4wk
## 233 0.6156011 233 0.6258870 Age1wk - Age4wk
## 234 1.0000000 234 1.0000000 Age1wk - Age4wk
## 235 0.2746386 235 0.3013966 Age1wk - Age4wk
## 236 1.0000000 236 1.0000000 Age1wk - Age4wk
## 237 0.3694538 237 0.3808525 Age1wk - Age4wk
## 238 0.9358425 238 0.9566489 Age1wk - Age4wk
## 239 0.7801185 239 0.7954931 Age1wk - Age4wk
## 240 1.0000000 240 1.0000000 Age1wk - Age4wk
## 241 1.0000000 241 1.0000000 Age1wk - Age4wk
## 242 0.1159113 242 0.1036166 Age1wk - Age4wk
## 243 1.0000000 243 1.0000000 Age1wk - Age4wk
## 244 1.0000000 244 1.0000000 Age1wk - Age4wk
## 245 0.2508434 245 0.2714430 Age1wk - Age4wk
## 246 1.0000000 246 1.0000000 Age1wk - Age4wk
## 247 0.1765727 247 0.1877824 Age1wk - Age4wk
## 248 0.1028244 248 0.1036166 Age1wk - Age4wk
## 249 0.3224437 249 0.3329325 Age1wk - Age4wk
## 250 1.0000000 250 1.0000000 Age1wk - Age4wk
## 251 1.0000000 251 1.0000000 Age1wk - Age4wk
## 252 0.4513805 252 0.4598838 Age1wk - Age4wk
## 253 0.9820394 253 1.0000000 Age1wk - Age4wk
## 254 0.1816424 254 0.1877824 Age1wk - Age4wk
## 255 0.1159113 255 0.1046682 Age1wk - Age4wk
## 256 1.0000000 256 1.0000000 Age1wk - Age4wk
## 257 1.0000000 257 1.0000000 Age1wk - Age4wk
## 258 0.6214929 258 0.6344084 Age1wk - Age4wk
## 259 0.9941052 259 1.0000000 Age1wk - Age4wk
## 260 1.0000000 260 1.0000000 Age1wk - Age4wk
## 261 0.6156011 261 0.6258870 Age1wk - Age4wk
## 262 1.0000000 262 1.0000000 Age1wk - Age4wk
## 263 0.7207527 263 0.7317515 Age1wk - Age4wk
## 264 1.0000000 264 1.0000000 Age1wk - Age4wk
## 265 0.2746386 265 0.3013966 Age1wk - Age4wk
## 266 1.0000000 266 1.0000000 Age1wk - Age4wk
## 267 0.9820394 267 1.0000000 Age1wk - Age4wk
## 268 0.2508434 268 0.2714430 Age1wk - Age4wk
## 269 1.0000000 269 1.0000000 Age1wk - Age4wk
## 270 0.8907850 270 0.9057715 Age1wk - Age4wk
## 271 0.4218229 271 0.4323511 Age1wk - Age4wk
## 272 0.6156011 272 0.6258870 Age1wk - Age4wk
## 273 0.2746386 273 0.3013966 Age1wk - Age4wk
## 274 0.6481130 274 0.6616225 Age1wk - Age4wk
## 275 0.2378919 275 0.2478953 Age1wk - Age4wk
## 276 0.1235801 276 0.1288975 Age1wk - Age4wk
## 277 0.2508434 277 0.2714430 Age1wk - Age4wk
## 278 0.2508434 278 0.2714430 Age1wk - Age4wk
## 279 1.0000000 279 1.0000000 Age1wk - Age4wk
## 280 0.3224437 280 0.3329325 Age1wk - Age4wk
## 281 0.3224437 281 0.3329325 Age1wk - Age4wk
## 282 1.0000000 282 1.0000000 Age1wk - Age4wk
## 283 0.1159113 283 0.1204399 Age1wk - Age4wk
## 284 0.2287792 284 0.2356633 Age1wk - Age4wk
## 285 0.3224437 285 0.3329325 Age1wk - Age4wk
## 286 0.7306438 286 0.7399152 Age1wk - Age4wk
## 287 0.9353785 287 0.9539383 Age1wk - Age4wk
## 288 1.0000000 288 1.0000000 Age1wk - Age4wk
## 289 1.0000000 289 1.0000000 Age1wk - Age4wk
## 290 0.5979575 290 0.6063418 Age1wk - Age4wk
## 291 0.2746386 291 0.3013966 Age1wk - Age4wk
## 292 1.0000000 292 1.0000000 Age1wk - Age4wk
## 293 0.6156011 293 0.6258870 Age1wk - Age4wk
## 294 0.6106036 294 0.6178069 Age1wk - Age4wk
## 295 1.0000000 295 1.0000000 Age1wk - Age4wk
## 296 1.0000000 296 1.0000000 Age1wk - Age4wk
## 297 1.0000000 297 1.0000000 Age1wk - Age4wk
## 298 0.2963575 298 0.3169020 Age1wk - Age4wk
## 299 1.0000000 299 1.0000000 Age1wk - Age4wk
## 300 1.0000000 300 1.0000000 Age1wk - Age4wk
## 301 0.4532870 301 0.4599598 Age1wk - Age4wk
## 302 0.6310966 302 0.6462709 Age1wk - Age4wk
## 303 0.6156011 303 0.6258870 Age1wk - Age4wk
## 304 0.1704707 304 0.1865056 Age1wk - Age4wk
## 305 1.0000000 305 1.0000000 Age1wk - Age4wk
## 306 0.8907850 306 0.9057715 Age1wk - Age4wk
## 307 0.2746386 307 0.3013966 Age1wk - Age4wk
## 308 0.2093308 308 0.2178862 Age1wk - Age4wk
## 309 1.0000000 309 1.0000000 Age1wk - Age4wk
## 310 0.3094772 310 0.3329325 Age1wk - Age4wk
## 311 0.2746386 311 0.3013966 Age1wk - Age4wk
## 312 0.1159113 312 0.1200430 Age1wk - Age4wk
## 313 1.0000000 313 1.0000000 Age1wk - Age4wk
## 314 0.3507103 314 0.3627825 Age1wk - Age4wk
## 315 0.9353785 315 0.9539383 Age1wk - Age4wk
## 316 0.9353785 316 0.9539383 Age1wk - Age4wk
## 317 0.9353785 317 0.9539383 Age1wk - Age4wk
## 318 0.5293155 318 0.5362826 Age1wk - Age4wk
## 319 1.0000000 319 1.0000000 Age1wk - Age4wk
## 320 1.0000000 320 1.0000000 Age1wk - Age4wk
## 321 1.0000000 321 1.0000000 Age1wk - Age4wk
## 322 0.9820394 322 1.0000000 Age1wk - Age4wk
## 323 0.1704707 323 0.1852144 Age1wk - Age4wk
## 324 0.9771507 324 1.0000000 Age1wk - Age4wk
## 325 1.0000000 325 1.0000000 Age1wk - Age4wk
## 326 0.7519977 326 0.7573074 Age1wk - Age4wk
## 327 0.7133253 327 0.7260649 Age1wk - Age4wk
## 328 0.3224437 328 0.3329325 Age1wk - Age4wk
## 329 0.2070032 329 0.2129872 Age1wk - Age4wk
## 330 1.0000000 330 1.0000000 Age1wk - Age4wk
## 331 1.0000000 331 1.0000000 Age1wk - Age4wk
## 332 0.9171184 332 0.9342001 Age1wk - Age4wk
## 333 0.8799327 333 0.8945728 Age1wk - Age4wk
## 334 0.1974004 334 0.2033831 Age1wk - Age4wk
## 335 0.4146536 335 0.4288112 Age1wk - Age4wk
## 336 0.5688616 336 0.5741101 Age1wk - Age4wk
## 337 0.8799327 337 0.8945728 Age1wk - Age4wk
## 338 0.2746386 338 0.3013966 Age1wk - Age4wk
## 339 0.6156011 339 0.6258870 Age1wk - Age4wk
## 340 0.2640309 340 0.2898203 Age1wk - Age4wk
## 341 1.0000000 341 1.0000000 Age1wk - Age4wk
## 342 0.6432889 342 0.6564839 Age1wk - Age4wk
## 343 0.8496096 343 0.8681566 Age1wk - Age4wk
## PValue_adj_withinNhood
## 1 0.7244973681
## 2 0.3968267906
## 3 0.7741359491
## 4 0.0420293274
## 5 0.0386138100
## 6 0.2708395280
## 7 0.0639943505
## 8 0.2211852757
## 9 0.9953704028
## 10 0.0062405123
## 11 0.8919487757
## 12 0.2678406963
## 13 0.0374681945
## 14 0.5748068106
## 15 0.7733500363
## 16 0.2765532447
## 17 0.9912076227
## 18 1.0000000000
## 19 0.2853819816
## 20 0.0353502325
## 21 0.0869404181
## 22 0.0524834302
## 23 0.7171302338
## 24 0.0108428632
## 25 0.1720370671
## 26 0.0091477149
## 27 0.9780272498
## 28 0.6036414471
## 29 0.9767181269
## 30 0.6863646865
## 31 0.4557169773
## 32 0.2523568330
## 33 0.8318362578
## 34 0.5448439125
## 35 0.5137949331
## 36 1.0000000000
## 37 0.0560797826
## 38 0.5697776543
## 39 0.2693758914
## 40 0.4230380362
## 41 0.8356781395
## 42 0.8555512418
## 43 0.9780272575
## 44 0.6847558982
## 45 0.0787437793
## 46 0.1269016175
## 47 1.0000000000
## 48 0.2769966488
## 49 1.0000000000
## 50 0.2692388196
## 51 0.7423692419
## 52 0.0378415327
## 53 0.3228740661
## 54 0.2327080509
## 55 0.3679097488
## 56 0.9835147909
## 57 0.2678944184
## 58 0.7549199073
## 59 0.3172909656
## 60 0.6175412149
## 61 0.9347211625
## 62 1.0000000000
## 63 0.0685552560
## 64 0.2678944184
## 65 0.0049759791
## 66 1.0000000000
## 67 0.9864414893
## 68 0.0081150618
## 69 0.0273335816
## 70 0.3635283273
## 71 0.2799818373
## 72 0.0188082991
## 73 1.0000000000
## 74 0.3224059266
## 75 1.0000000000
## 76 0.0066495952
## 77 1.0000000000
## 78 0.7681741709
## 79 0.8426973727
## 80 0.0223297923
## 81 0.0672205614
## 82 0.2765359354
## 83 1.0000000000
## 84 0.1921279246
## 85 0.0088142054
## 86 1.0000000000
## 87 0.1381776906
## 88 0.0847391255
## 89 0.9505375356
## 90 1.0000000000
## 91 0.1514559101
## 92 0.6518187452
## 93 0.2477785104
## 94 0.7687688689
## 95 0.0251016854
## 96 0.9321306865
## 97 0.0012335734
## 98 0.0743393180
## 99 0.0074947403
## 100 1.0000000000
## 101 0.0606209534
## 102 1.0000000000
## 103 1.0000000000
## 104 0.2332839513
## 105 1.0000000000
## 106 0.5022470897
## 107 0.6716119050
## 108 0.1035862918
## 109 0.0218891903
## 110 0.0096162420
## 111 0.8762435723
## 112 0.9542238290
## 113 0.4684998110
## 114 0.5811499827
## 115 1.0000000000
## 116 0.8647793384
## 117 1.0000000000
## 118 0.2552217491
## 119 0.0141438691
## 120 0.3566757461
## 121 0.3825695460
## 122 0.2416906375
## 123 0.5248559278
## 124 0.2405395627
## 125 0.2387311787
## 126 1.0000000000
## 127 0.0481546893
## 128 0.0034464866
## 129 0.0542747207
## 130 0.0149099714
## 131 0.0289306568
## 132 1.0000000000
## 133 0.4394067523
## 134 0.9348376806
## 135 1.0000000000
## 136 0.2880973078
## 137 0.2775565213
## 138 0.2678944176
## 139 0.0815501153
## 140 0.6221728371
## 141 0.5155731990
## 142 0.0509634212
## 143 0.1044811113
## 144 0.2796696834
## 145 0.0854737563
## 146 0.7254413918
## 147 0.7410109769
## 148 0.0032803505
## 149 0.2678944172
## 150 0.9987166236
## 151 0.0856526837
## 152 0.3500195087
## 153 0.0099090918
## 154 1.0000000000
## 155 1.0000000000
## 156 0.7546866450
## 157 0.0040552053
## 158 0.1763041664
## 159 0.6876450759
## 160 0.9355393360
## 161 1.0000000000
## 162 0.2678944183
## 163 0.9140711029
## 164 0.3353861575
## 165 0.2717592080
## 166 0.8943543371
## 167 0.2247036814
## 168 0.9801589808
## 169 1.0000000000
## 170 0.4982380164
## 171 0.0874264151
## 172 0.0025300269
## 173 0.0431070809
## 174 1.0000000000
## 175 0.0096023485
## 176 0.1625045704
## 177 0.5013966180
## 178 0.0008879162
## 179 0.0017078414
## 180 0.9143431418
## 181 0.2678944184
## 182 0.0123151771
## 183 0.8123749416
## 184 0.3703703880
## 185 1.0000000000
## 186 0.4407778678
## 187 0.5802910091
## 188 1.0000000000
## 189 0.3504893744
## 190 0.8356991819
## 191 0.0815338398
## 192 0.2468673438
## 193 0.8367360063
## 194 0.2192937441
## 195 0.3791679049
## 196 0.1638792936
## 197 1.0000000000
## 198 0.0346896585
## 199 1.0000000000
## 200 0.4118540236
## 201 0.4083423957
## 202 0.1264269397
## 203 0.3677518407
## 204 0.0131020605
## 205 1.0000000000
## 206 0.4951329656
## 207 0.2707529850
## 208 0.1238176360
## 209 0.4003276345
## 210 0.6911559990
## 211 0.0703767388
## 212 0.8408614922
## 213 0.8658726458
## 214 0.0254302673
## 215 0.0538839436
## 216 0.3037334699
## 217 0.1553346859
## 218 0.8801290437
## 219 0.0856947784
## 220 0.1351218277
## 221 0.2788506707
## 222 0.7457915157
## 223 1.0000000000
## 224 1.0000000000
## 225 1.0000000000
## 226 0.0568493799
## 227 0.9618655201
## 228 0.1415972887
## 229 1.0000000000
## 230 0.9400285969
## 231 0.1593006943
## 232 0.0543494965
## 233 0.2681124255
## 234 1.0000000000
## 235 0.0566716255
## 236 0.7093706698
## 237 0.1035824867
## 238 0.5792043308
## 239 0.4228477645
## 240 0.8321666153
## 241 0.6817446313
## 242 0.0016713512
## 243 1.0000000000
## 244 1.0000000000
## 245 0.0378535621
## 246 1.0000000000
## 247 0.0159584625
## 248 0.0002997796
## 249 0.0813590526
## 250 0.7668840292
## 251 1.0000000000
## 252 0.1376332700
## 253 0.6298794729
## 254 0.0169462337
## 255 0.0021875590
## 256 1.0000000000
## 257 0.6559288634
## 258 0.2872391837
## 259 0.6405167911
## 260 1.0000000000
## 261 0.2332105986
## 262 1.0000000000
## 263 0.3624319322
## 264 0.8826813597
## 265 0.0548379526
## 266 1.0000000000
## 267 0.6275263634
## 268 0.0387600615
## 269 0.7352326442
## 270 0.5219193511
## 271 0.1217506264
## 272 0.2518806094
## 273 0.0556232024
## 274 0.3079954004
## 275 0.0305167441
## 276 0.0050440877
## 277 0.0375801809
## 278 0.0354924259
## 279 0.9817631196
## 280 0.0793470892
## 281 0.0805289751
## 282 1.0000000000
## 283 0.0038393892
## 284 0.0280137814
## 285 0.0773361395
## 286 0.3778629412
## 287 0.5641216667
## 288 0.7703955531
## 289 1.0000000000
## 290 0.2057113418
## 291 0.0508021624
## 292 1.0000000000
## 293 0.2678944522
## 294 0.2118420747
## 295 0.8764315958
## 296 0.6630622496
## 297 0.6821124376
## 298 0.0630731786
## 299 0.9063559887
## 300 0.6590283795
## 301 0.1400828630
## 302 0.2943891056
## 303 0.2766243060
## 304 0.0147807938
## 305 0.7462288525
## 306 0.5220052115
## 307 0.0547211060
## 308 0.0231911638
## 309 0.8612987134
## 310 0.0699115942
## 311 0.0548046199
## 312 0.0035175493
## 313 1.0000000000
## 314 0.0961130385
## 315 0.5615543744
## 316 0.5667175268
## 317 0.5699536374
## 318 0.1774672880
## 319 1.0000000000
## 320 0.8378557986
## 321 1.0000000000
## 322 0.6287128477
## 323 0.0137622123
## 324 0.6124996870
## 325 0.9453417300
## 326 0.3958274007
## 327 0.3535431364
## 328 0.0829187826
## 329 0.0217729794
## 330 0.8087083603
## 331 0.7638926936
## 332 0.5454581853
## 333 0.5046102345
## 334 0.0195673894
## 335 0.1184724660
## 336 0.1940431771
## 337 0.5053840991
## 338 0.0469469688
## 339 0.2193689719
## 340 0.0429491365
## 341 0.8385667366
## 342 0.3038273979
## 343 0.4731062196
##
## $artifacts$design_df
## Sample Age
## 1_1wk 1_1wk 1wk
## 1_4wk 1_4wk 4wk
## 1_16wk 1_16wk 16wk
## 1_32wk 1_32wk 32wk
## 1_52wk 1_52wk 52wk
## 2_32wk 2_32wk 32wk
## 2_4wk 2_4wk 4wk
## 2_1wk 2_1wk 1wk
## 2_16wk 2_16wk 16wk
## 2_52wk 2_52wk 52wk
## 3_4wk 3_4wk 4wk
## 3_1wk 3_1wk 1wk
## 3_52wk 3_52wk 52wk
## 3_16wk 3_16wk 16wk
## 3_32wk 3_32wk 32wk
## 4_1wk 4_1wk 1wk
## 4_16wk 4_16wk 16wk
## 4_4wk 4_4wk 4wk
## 4_32wk 4_32wk 32wk
## 4_52wk 4_52wk 52wk
## 5_32wk 5_32wk 32wk
## 5_52wk 5_52wk 52wk
## 5_1wk 5_1wk 1wk
## 5_4wk 5_4wk 4wk
## 5_16wk 5_16wk 16wk
##
## $artifacts$formula
## [1] "~0 + Age"
##
## $artifacts$contrasts
## [1] "Age1wk - Age4wk"
##
##
## $params
## $params$k1
## [1] 11
##
## $params$k2
## [1] 11
##
## $params$d1
## [1] 40
##
## $params$d2
## [1] 40
##
## $params$d3
## [1] 30
##
## $params$prop
## [1] 0.2
##
## $params$overlap
## [1] 1
##
## $params$per_contrast
## [1] TRUE
##
## $params$is_refined
## [1] TRUE
##
## $params$refinement_scheme
## [1] "graph"
##
## $params$adjustment
## [1] "BH"
##
## $params$glmm
## [1] FALSE
##
## $params$random_effect
## NULL
##
## $params$glmm_solver
## [1] "Fisher"
##
## $params$REML
## [1] TRUE
##
## $params$max.iters
## [1] 50
##
## $params$fail.on.error
## [1] FALSE
##
## $params$seed
## [1] 2025
##
##
## $summary
## $summary$n_nhood_results
## [1] 343
##
## $summary$n_samples
## [1] 25
##
##
## $created_at
## [1] "2026-05-31 05:03:09 UTC"
##
## $da_results
## logFC logCPM F PValue
## 1 -0.424880954 13.66075 1.242344e-01 0.7244973681
## 2 -1.117822619 13.37924 7.180106e-01 0.3968267906
## 3 0.368076626 13.57295 8.235778e-02 0.7741359491
## 4 -2.862363545 13.87550 4.135570e+00 0.0420293274
## 5 -2.829461820 13.65808 4.279423e+00 0.0386138100
## 6 -1.417717985 13.55053 1.212686e+00 0.2708395280
## 7 2.411644567 13.35979 3.431824e+00 0.0639943505
## 8 -1.528117211 13.49564 1.496937e+00 0.2211852757
## 9 -0.004906545 13.40558 3.366998e-05 0.9953704028
## 10 -3.980828065 13.38533 7.484133e+00 0.0062405123
## 11 -0.176192860 13.60726 1.845353e-02 0.8919487757
## 12 -1.473387179 13.39248 1.227972e+00 0.2678406963
## 13 -2.864754953 13.43724 4.330685e+00 0.0374681945
## 14 -0.665538997 13.55753 3.147359e-01 0.5748068106
## 15 -0.325235904 13.75332 8.294807e-02 0.7733500363
## 16 -1.204195394 13.64289 1.184139e+00 0.2765532447
## 17 -0.015332105 13.41399 1.214456e-04 0.9912076227
## 18 0.000000000 13.52487 0.000000e+00 1.0000000000
## 19 1.251604656 13.54059 1.141458e+00 0.2853819816
## 20 2.759813107 13.47791 4.429930e+00 0.0353502325
## 21 2.070528473 13.65160 2.930971e+00 0.0869404181
## 22 -2.579254060 13.39941 3.761596e+00 0.0524834302
## 23 -0.466985007 13.33484 1.312698e-01 0.7171302338
## 24 3.522365090 13.45113 6.494436e+00 0.0108428632
## 25 -1.772402042 13.71854 1.865492e+00 0.1720370671
## 26 -3.721712027 13.71345 6.797619e+00 0.0091477149
## 27 0.169448871 13.36126 1.342907e-02 0.9780272498
## 28 0.623537211 13.56022 2.695635e-01 0.6036414471
## 29 -0.032617153 13.43381 8.517471e-04 0.9767181269
## 30 0.441833833 13.52357 1.630629e-01 0.6863646865
## 31 -0.891295529 13.77306 5.564567e-01 0.4557169773
## 32 -1.482867854 13.65031 1.310430e+00 0.2523568330
## 33 0.253254184 13.99112 4.509472e-02 0.8318362578
## 34 0.761754415 13.34543 3.666721e-01 0.5448439125
## 35 -0.844614803 13.60263 4.263750e-01 0.5137949331
## 36 0.000000000 13.63346 0.000000e+00 1.0000000000
## 37 -2.574031743 13.61366 3.650923e+00 0.0560797826
## 38 0.744413041 13.42664 3.230858e-01 0.5697776543
## 39 -1.185717566 13.47918 1.220120e+00 0.2693758914
## 40 0.916331256 13.82054 6.419369e-01 0.4230380362
## 41 -0.251978393 13.54110 4.302831e-02 0.8356781395
## 42 -0.223363849 13.60682 3.314110e-02 0.8555512418
## 43 -0.057057273 13.46196 1.914739e-03 0.9780272575
## 44 0.518061348 13.38562 1.648353e-01 0.6847558982
## 45 -2.258750850 13.71189 3.091563e+00 0.0787437793
## 46 -1.838154533 13.36053 2.330569e+00 0.1269016175
## 47 0.000000000 13.52870 0.000000e+00 1.0000000000
## 48 -1.188698301 13.60336 1.181955e+00 0.2769966488
## 49 0.000000000 13.77713 0.000000e+00 1.0000000000
## 50 -1.185802257 13.48131 1.220819e+00 0.2692388196
## 51 0.373582963 13.81322 1.080639e-01 0.7423692419
## 52 -2.836136439 13.47682 4.313801e+00 0.0378415327
## 53 -1.246600777 13.55548 9.774095e-01 0.3228740661
## 54 1.238345509 13.59173 1.424484e+00 0.2327080509
## 55 1.071904932 13.52451 8.108193e-01 0.3679097488
## 56 0.122787309 13.38286 9.275920e-03 0.9835147909
## 57 -1.202367177 13.46901 1.230838e+00 0.2678944184
## 58 0.381292023 13.50587 9.745086e-02 0.7549199073
## 59 1.267997488 13.48212 1.000227e+00 0.3172909656
## 60 -0.681563634 13.82784 2.493612e-01 0.6175412149
## 61 0.098821777 13.37891 6.709147e-03 0.9347211625
## 62 0.000000000 13.36367 0.000000e+00 1.0000000000
## 63 -2.512702862 13.63493 3.318322e+00 0.0685552560
## 64 -1.201211763 13.38506 1.273519e+00 0.2678944184
## 65 -4.076428534 13.72174 7.893261e+00 0.0049759791
## 66 0.000000000 13.40962 0.000000e+00 1.0000000000
## 67 0.019982643 13.74482 2.888134e-04 0.9864414893
## 68 -3.751840144 13.53703 7.011996e+00 0.0081150618
## 69 -3.068945742 13.42384 4.871700e+00 0.0273335816
## 70 1.180128789 13.40490 8.257773e-01 0.3635283273
## 71 -1.189703306 13.71189 1.167362e+00 0.2799818373
## 72 3.214770613 13.38068 5.521875e+00 0.0188082991
## 73 0.000000000 13.91102 0.000000e+00 1.0000000000
## 74 -1.357412247 13.42397 9.793027e-01 0.3224059266
## 75 0.000000000 13.31744 0.000000e+00 1.0000000000
## 76 -4.050595281 13.92972 7.369754e+00 0.0066495952
## 77 0.000000000 13.45196 0.000000e+00 1.0000000000
## 78 0.350342673 13.43104 8.689270e-02 0.7681741709
## 79 -0.222803764 13.75660 3.938317e-02 0.8426973727
## 80 -3.145858560 13.54091 5.222271e+00 0.0223297923
## 81 -2.482608170 13.44524 3.350681e+00 0.0672205614
## 82 -1.204292534 13.66093 1.184224e+00 0.2765359354
## 83 0.000000000 13.44745 0.000000e+00 1.0000000000
## 84 -1.688098824 13.76266 1.701559e+00 0.1921279246
## 85 -3.703001112 13.51270 6.864023e+00 0.0088142054
## 86 0.000000000 13.49337 0.000000e+00 1.0000000000
## 87 -1.798180840 13.50322 2.198649e+00 0.1381776906
## 88 -2.242607368 13.45573 2.972439e+00 0.0847391255
## 89 0.125948815 13.39763 1.009465e-02 0.9505375356
## 90 0.000000000 13.51051 0.000000e+00 1.0000000000
## 91 1.689734201 13.90862 2.057984e+00 0.1514559101
## 92 0.531750415 13.53974 2.036327e-01 0.6518187452
## 93 1.392989067 13.50140 1.336013e+00 0.2477785104
## 94 -0.425620309 13.40358 8.643441e-02 0.7687688689
## 95 2.911714110 13.49798 5.019058e+00 0.0251016854
## 96 -0.103310636 13.51971 7.253509e-03 0.9321306865
## 97 4.645694875 13.41742 1.044808e+01 0.0012335734
## 98 2.276735586 13.48771 3.185481e+00 0.0743393180
## 99 -3.896827775 13.77632 7.154646e+00 0.0074947403
## 100 0.000000000 13.57378 0.000000e+00 1.0000000000
## 101 2.491426644 13.40460 3.521474e+00 0.0606209534
## 102 0.000000000 13.36593 0.000000e+00 1.0000000000
## 103 0.000000000 13.38795 0.000000e+00 1.0000000000
## 104 -1.429238917 13.74524 1.420977e+00 0.2332839513
## 105 0.000000000 13.50619 0.000000e+00 1.0000000000
## 106 -0.888319018 13.40719 4.502326e-01 0.5022470897
## 107 0.526410077 13.45027 1.797379e-01 0.6716119050
## 108 -2.188586199 13.52521 2.650146e+00 0.1035862918
## 109 -3.272433596 13.42831 5.256968e+00 0.0218891903
## 110 -3.744580182 13.42334 6.708405e+00 0.0096162420
## 111 -0.201206321 13.52823 2.425454e-02 0.8762435723
## 112 0.050160184 13.42569 3.295395e-03 0.9542238290
## 113 -0.883005823 13.61723 5.255705e-01 0.4684998110
## 114 -0.693284835 13.54719 3.044082e-01 0.5811499827
## 115 0.000000000 13.58075 0.000000e+00 1.0000000000
## 116 -0.223380264 13.49849 2.900204e-02 0.8647793384
## 117 0.000000000 13.40962 0.000000e+00 1.0000000000
## 118 -1.533255109 13.38229 1.294709e+00 0.2552217491
## 119 3.377092321 13.41682 6.023178e+00 0.0141438691
## 120 -1.193437091 13.72690 8.496784e-01 0.3566757461
## 121 -1.124099327 13.32192 7.625266e-01 0.3825695460
## 122 1.384943428 13.69011 1.370943e+00 0.2416906375
## 123 -0.828401318 13.50617 4.043823e-01 0.5248559278
## 124 -1.524385781 13.48467 1.377668e+00 0.2405395627
## 125 -1.472351651 13.52659 1.388312e+00 0.2387311787
## 126 0.000000000 13.99179 0.000000e+00 1.0000000000
## 127 2.629388104 13.45333 3.905975e+00 0.0481546893
## 128 3.915311769 13.56029 8.560569e+00 0.0034464866
## 129 -2.560054117 13.41227 3.705500e+00 0.0542747207
## 130 -3.438458368 13.73183 5.930068e+00 0.0149099714
## 131 -3.077919719 13.47893 4.773743e+00 0.0289306568
## 132 0.000000000 13.64616 0.000000e+00 1.0000000000
## 133 0.950328974 13.47432 5.979007e-01 0.4394067523
## 134 0.098538182 13.37656 6.685164e-03 0.9348376806
## 135 0.000000000 13.97159 0.000000e+00 1.0000000000
## 136 -1.324802122 13.53687 1.128667e+00 0.2880973078
## 137 -1.188718567 13.60745 1.179203e+00 0.2775565213
## 138 -1.186914885 13.51157 1.235116e+00 0.2678944176
## 139 -2.240457134 13.53597 3.034627e+00 0.0815501153
## 140 0.621646147 13.42053 2.428474e-01 0.6221728371
## 141 0.906703741 13.44685 4.227834e-01 0.5155731990
## 142 -2.595803093 13.53630 3.810811e+00 0.0509634212
## 143 -2.212850425 13.57491 2.636473e+00 0.1044811113
## 144 -1.189643431 13.70679 1.168879e+00 0.2796696834
## 145 -2.254301116 13.67604 2.958472e+00 0.0854737563
## 146 -0.399918474 13.77278 1.233487e-01 0.7254413918
## 147 0.381848164 13.71829 1.092489e-01 0.7410109769
## 148 -4.293656540 13.59428 8.650664e+00 0.0032803505
## 149 -1.171432575 13.37771 1.257888e+00 0.2678944172
## 150 0.002114379 13.74663 2.587379e-06 0.9987166236
## 151 -2.226398894 13.43367 2.955089e+00 0.0856526837
## 152 -1.209450348 13.32701 8.735057e-01 0.3500195087
## 153 3.565903263 13.46420 6.654877e+00 0.0099090918
## 154 0.000000000 13.45140 0.000000e+00 1.0000000000
## 155 0.000000000 13.66416 0.000000e+00 1.0000000000
## 156 0.362978077 13.54463 9.764261e-02 0.7546866450
## 157 3.886316627 13.61152 8.264505e+00 0.0040552053
## 158 -1.766103700 13.52619 1.828883e+00 0.1763041664
## 159 -0.501424028 13.44845 1.616602e-01 0.6876450759
## 160 -0.087440139 13.48441 6.541658e-03 0.9355393360
## 161 0.000000000 13.86004 0.000000e+00 1.0000000000
## 162 -1.202948077 13.53331 1.235690e+00 0.2678944183
## 163 0.126028336 13.70955 1.164433e-02 0.9140711029
## 164 -1.192014580 13.53860 9.281189e-01 0.3353861575
## 165 -1.502425869 13.45352 1.208040e+00 0.2717592080
## 166 -0.167468828 13.44055 1.763621e-02 0.8943543371
## 167 -1.628967656 13.34295 1.474342e+00 0.2247036814
## 168 -0.005158776 13.43394 6.185418e-04 0.9801589808
## 169 0.000000000 13.60817 0.000000e+00 1.0000000000
## 170 0.847656077 13.45467 4.587363e-01 0.4982380164
## 171 -2.235746397 13.61874 2.921969e+00 0.0874264151
## 172 -4.519928792 13.45216 9.125479e+00 0.0025300269
## 173 2.534663268 13.52782 4.092716e+00 0.0431070809
## 174 0.000000000 13.61327 0.000000e+00 1.0000000000
## 175 3.356959879 13.65586 6.710986e+00 0.0096023485
## 176 -1.821585953 13.95295 1.951183e+00 0.1625045704
## 177 -0.879703102 13.35995 4.520269e-01 0.5013966180
## 178 4.789226849 13.45815 1.105753e+01 0.0008879162
## 179 -4.596204439 13.50774 9.847491e+00 0.0017078414
## 180 0.121679352 13.61037 1.157044e-02 0.9143431418
## 181 -1.201051210 13.33962 1.335467e+00 0.2678944184
## 182 -3.603619302 13.39472 6.268238e+00 0.0123151771
## 183 -0.294809578 13.50575 5.634568e-02 0.8123749416
## 184 -1.162697830 13.37973 8.025269e-01 0.3703703880
## 185 0.000000000 13.81226 0.000000e+00 1.0000000000
## 186 -0.971714712 13.53391 5.943255e-01 0.4407778678
## 187 -0.684553806 13.63758 3.057935e-01 0.5802910091
## 188 0.000000000 13.68603 0.000000e+00 1.0000000000
## 189 1.130379002 13.50436 8.718035e-01 0.3504893744
## 190 -0.272197146 13.63700 4.301713e-02 0.8356991819
## 191 -2.240781558 13.54103 3.034951e+00 0.0815338398
## 192 1.367062279 13.55996 1.341174e+00 0.2468673438
## 193 -0.275028185 13.45096 4.246819e-02 0.8367360063
## 194 1.371160152 13.70081 1.509263e+00 0.2192937441
## 195 -1.184995847 13.39601 7.734980e-01 0.3791679049
## 196 -1.918463089 13.62171 1.938475e+00 0.1638792936
## 197 0.000000000 13.51508 0.000000e+00 1.0000000000
## 198 -2.860601683 13.50740 4.462162e+00 0.0346896585
## 199 0.000000000 13.51397 0.000000e+00 1.0000000000
## 200 0.995836034 13.50286 6.735245e-01 0.4118540236
## 201 -1.004547699 13.55005 6.837056e-01 0.4083423957
## 202 1.884987801 13.51184 2.336406e+00 0.1264269397
## 203 1.023058942 13.76308 8.113541e-01 0.3677518407
## 204 3.464091303 13.45266 6.158488e+00 0.0131020605
## 205 0.000000000 13.74156 0.000000e+00 1.0000000000
## 206 -0.882980583 13.59076 4.654024e-01 0.4951329656
## 207 -1.402994531 13.49527 1.213124e+00 0.2707529850
## 208 1.978626874 13.46933 2.368934e+00 0.1238176360
## 209 0.967442992 13.77281 7.074300e-01 0.4003276345
## 210 -0.477408152 13.62649 1.578501e-01 0.6911559990
## 211 2.338989984 13.55734 3.275232e+00 0.0703767388
## 212 0.246223681 13.47759 4.032034e-02 0.8408614922
## 213 0.203306790 13.65588 2.853049e-02 0.8658726458
## 214 -3.095781503 13.38677 4.996528e+00 0.0254302673
## 215 -2.604552041 13.68583 3.717569e+00 0.0538839436
## 216 -1.288113019 13.64621 1.057889e+00 0.3037334699
## 217 -1.917488676 13.45381 2.019510e+00 0.1553346859
## 218 0.170826650 13.87011 2.274403e-02 0.8801290437
## 219 -2.227788316 13.45941 2.954295e+00 0.0856947784
## 220 -1.998653948 13.40175 2.233177e+00 0.1351218277
## 221 -1.262350106 13.78209 1.172869e+00 0.2788506707
## 222 -0.418667127 13.40831 1.051099e-01 0.7457915157
## 223 0.000000000 13.64325 0.000000e+00 1.0000000000
## 224 0.000000000 13.38399 0.000000e+00 1.0000000000
## 225 0.000000000 13.68194 0.000000e+00 1.0000000000
## 226 2.540943709 13.43549 3.628218e+00 0.0568493799
## 227 0.030120426 13.51820 2.286221e-03 0.9618655201
## 228 -1.804226187 13.45374 2.161012e+00 0.1415972887
## 229 0.000000000 13.41787 0.000000e+00 1.0000000000
## 230 0.089685702 13.45690 5.660558e-03 0.9400285969
## 231 -1.883063680 13.33688 1.981282e+00 0.1593006943
## 232 -2.488295910 13.54323 3.703201e+00 0.0543494965
## 233 -1.202093576 13.44827 1.226578e+00 0.2681124255
## 234 0.000000000 13.75786 0.000000e+00 1.0000000000
## 235 -2.555632030 13.44727 3.633433e+00 0.0566716255
## 236 -0.439113494 13.58434 1.389179e-01 0.7093706698
## 237 1.994304500 13.51333 2.650205e+00 0.1035824867
## 238 -0.690441808 13.57915 3.075520e-01 0.5792043308
## 239 0.916396683 13.72871 6.424639e-01 0.4228477645
## 240 0.298424457 13.41960 4.491505e-02 0.8321666153
## 241 -0.518479256 13.43662 1.681829e-01 0.6817446313
## 242 -4.605680901 13.75034 9.887286e+00 0.0016713512
## 243 0.000000000 13.78072 0.000000e+00 1.0000000000
## 244 0.000000000 13.36415 0.000000e+00 1.0000000000
## 245 -2.856727901 13.63482 4.313260e+00 0.0378535621
## 246 0.000000000 13.47492 0.000000e+00 1.0000000000
## 247 -3.436700504 13.67958 5.810328e+00 0.0159584625
## 248 5.164141698 13.56788 1.308519e+01 0.0002997796
## 249 -2.274918162 13.42886 3.038436e+00 0.0813590526
## 250 0.372717041 13.40032 8.789145e-02 0.7668840292
## 251 0.000000000 13.47219 0.000000e+00 1.0000000000
## 252 -1.839919711 13.44875 2.204737e+00 0.1376332700
## 253 -0.623790677 13.53936 2.322451e-01 0.6298794729
## 254 -3.245523233 13.33016 5.704720e+00 0.0169462337
## 255 -4.453097346 13.57873 9.392209e+00 0.0021875590
## 256 0.000000000 13.35504 0.000000e+00 1.0000000000
## 257 0.528970590 13.53670 1.985241e-01 0.6559288634
## 258 -1.383505065 13.64084 1.132693e+00 0.2872391837
## 259 -0.541950770 13.79529 2.180863e-01 0.6405167911
## 260 0.000000000 13.56247 0.000000e+00 1.0000000000
## 261 -1.565028125 13.85595 1.421423e+00 0.2332105986
## 262 0.000000000 13.48125 0.000000e+00 1.0000000000
## 263 -1.233077916 13.39357 8.295595e-01 0.3624319322
## 264 -0.167410678 13.64393 2.177882e-02 0.8826813597
## 265 -2.597883443 13.63049 3.688266e+00 0.0548379526
## 266 0.000000000 13.45196 0.000000e+00 1.0000000000
## 267 0.564407210 13.62651 2.354513e-01 0.6275263634
## 268 -2.921220209 13.43771 4.272994e+00 0.0387600615
## 269 -0.403328968 13.59250 1.143704e-01 0.7352326442
## 270 0.857531727 13.40426 4.101410e-01 0.5219193511
## 271 -1.838521101 13.33566 2.395247e+00 0.1217506264
## 272 1.432587820 13.41865 1.313064e+00 0.2518806094
## 273 2.561980921 13.49912 3.664550e+00 0.0556232024
## 274 -1.273003363 13.49613 1.039407e+00 0.3079954004
## 275 -3.040088418 13.60130 4.681882e+00 0.0305167441
## 276 -4.067630206 13.63741 7.868646e+00 0.0050440877
## 277 2.744463519 13.47787 4.325602e+00 0.0375801809
## 278 -2.841470138 13.54390 4.423074e+00 0.0354924259
## 279 0.022954053 13.56449 5.225505e-04 0.9817631196
## 280 -2.263153001 13.40097 3.079140e+00 0.0793470892
## 281 -2.266400521 13.48922 3.055096e+00 0.0805289751
## 282 0.000000000 13.74002 0.000000e+00 1.0000000000
## 283 -4.269673792 13.47778 8.363960e+00 0.0038393892
## 284 -3.064408324 13.43721 4.829270e+00 0.0280137814
## 285 -2.242605199 13.36316 3.120951e+00 0.0773361395
## 286 -1.261074402 13.78086 7.777438e-01 0.3778629412
## 287 0.708080534 13.45800 3.326501e-01 0.5641216667
## 288 0.361743724 13.87130 8.518756e-02 0.7703955531
## 289 0.000000000 13.41102 0.000000e+00 1.0000000000
## 290 -1.549473965 13.80476 1.601658e+00 0.2057113418
## 291 -2.585170487 13.37433 3.816123e+00 0.0508021624
## 292 0.000000000 13.87075 0.000000e+00 1.0000000000
## 293 -1.561259744 13.42378 1.495283e+00 0.2678944522
## 294 1.371522464 13.49454 1.585263e+00 0.2118420747
## 295 -0.204898348 13.47161 2.418030e-02 0.8764315958
## 296 0.516669819 13.73015 1.898415e-01 0.6630622496
## 297 -0.533177853 13.35981 1.677719e-01 0.6821124376
## 298 -2.543913691 13.48659 3.455796e+00 0.0630731786
## 299 0.134526976 13.65110 1.383928e-02 0.9063559887
## 300 -0.605587895 13.32302 2.047466e-01 0.6590283795
## 301 -1.813544231 13.46094 2.177553e+00 0.1400828630
## 302 -1.345893302 13.59251 1.099608e+00 0.2943891056
## 303 -1.203587137 13.62459 1.183788e+00 0.2766243060
## 304 3.213393151 13.66743 5.945418e+00 0.0147807938
## 305 0.393183553 13.45714 1.047357e-01 0.7462288525
## 306 0.797914761 13.42752 4.099718e-01 0.5220052115
## 307 -2.587483646 13.44173 3.691826e+00 0.0547211060
## 308 3.113997446 13.48557 5.156442e+00 0.0231911638
## 309 0.216590758 13.36617 3.052979e-02 0.8612987134
## 310 -2.542200977 13.77976 3.286121e+00 0.0699115942
## 311 -2.585234992 13.77059 3.689281e+00 0.0548046199
## 312 -4.358021041 13.87422 8.523372e+00 0.0035175493
## 313 0.000000000 13.40480 0.000000e+00 1.0000000000
## 314 -2.209603410 13.30578 2.769647e+00 0.0961130385
## 315 0.683767386 13.85598 3.370529e-01 0.5615543744
## 316 0.687328106 13.49532 3.282375e-01 0.5667175268
## 317 -0.690269095 13.50355 3.227912e-01 0.5699536374
## 318 -1.886221206 13.39172 1.819080e+00 0.1774672880
## 319 0.000000000 13.55688 0.000000e+00 1.0000000000
## 320 0.243650930 13.36793 4.187945e-02 0.8378557986
## 321 0.000000000 13.76151 0.000000e+00 1.0000000000
## 322 0.636938385 13.47072 2.338313e-01 0.6287128477
## 323 -3.443484840 13.53760 6.071520e+00 0.0137622123
## 324 0.603441835 13.50057 2.565744e-01 0.6124996870
## 325 -0.070062488 13.65374 4.700496e-03 0.9453417300
## 326 -1.102001219 13.42819 7.210559e-01 0.3958274007
## 327 -1.129900564 13.53967 8.608158e-01 0.3535431364
## 328 -2.264927719 13.45615 3.007621e+00 0.0829187826
## 329 -3.229997791 13.45355 5.266240e+00 0.0217729794
## 330 -0.329393912 13.43705 5.861338e-02 0.8087083603
## 331 -0.380359107 13.37328 9.023108e-02 0.7638926936
## 332 -0.707978650 13.81118 3.655532e-01 0.5454581853
## 333 -0.820495005 13.65112 4.452741e-01 0.5046102345
## 334 3.221109314 13.44767 5.452647e+00 0.0195673894
## 335 -2.099209133 13.61887 2.438011e+00 0.1184724660
## 336 1.730693788 13.44189 1.686980e+00 0.1940431771
## 337 -0.850157785 13.43439 4.436590e-01 0.5053840991
## 338 2.749166600 13.39038 3.948712e+00 0.0469469688
## 339 -1.549258919 13.54426 1.508770e+00 0.2193689719
## 340 2.693552947 13.44685 4.098926e+00 0.0429491365
## 341 -0.255149378 13.43712 4.150790e-02 0.8385667366
## 342 -1.353047618 13.31144 1.057478e+00 0.3038273979
## 343 -0.937536489 13.42697 5.147687e-01 0.4731062196
## FDR Nhood SpatialFDR contrast
## 1 1.0000000 1 1.0000000 Age1wk - Age4wk
## 2 0.7519977 2 0.7573074 Age1wk - Age4wk
## 3 1.0000000 3 1.0000000 Age1wk - Age4wk
## 4 0.2640309 4 0.2898203 Age1wk - Age4wk
## 5 0.2508434 5 0.2714430 Age1wk - Age4wk
## 6 0.6156011 6 0.6258870 Age1wk - Age4wk
## 7 0.2966225 7 0.3169020 Age1wk - Age4wk
## 8 0.6156011 8 0.6258870 Age1wk - Age4wk
## 9 1.0000000 9 1.0000000 Age1wk - Age4wk
## 10 0.1425507 10 0.1436379 Age1wk - Age4wk
## 11 1.0000000 11 1.0000000 Age1wk - Age4wk
## 12 0.6156011 12 0.6258870 Age1wk - Age4wk
## 13 0.2508434 13 0.2714430 Age1wk - Age4wk
## 14 0.9358425 14 0.9553453 Age1wk - Age4wk
## 15 1.0000000 15 1.0000000 Age1wk - Age4wk
## 16 0.6156011 16 0.6258870 Age1wk - Age4wk
## 17 1.0000000 17 1.0000000 Age1wk - Age4wk
## 18 1.0000000 18 1.0000000 Age1wk - Age4wk
## 19 0.6214929 19 0.6344084 Age1wk - Age4wk
## 20 0.2508434 20 0.2714430 Age1wk - Age4wk
## 21 0.3224437 21 0.3344722 Age1wk - Age4wk
## 22 0.2746386 22 0.3013966 Age1wk - Age4wk
## 23 1.0000000 23 1.0000000 Age1wk - Age4wk
## 24 0.1549626 24 0.1717565 Age1wk - Age4wk
## 25 0.5222010 25 0.5288930 Age1wk - Age4wk
## 26 0.1477747 26 0.1615543 Age1wk - Age4wk
## 27 1.0000000 27 1.0000000 Age1wk - Age4wk
## 28 0.9675188 28 0.9903370 Age1wk - Age4wk
## 29 1.0000000 29 1.0000000 Age1wk - Age4wk
## 30 1.0000000 30 1.0000000 Age1wk - Age4wk
## 31 0.8270419 31 0.8479031 Age1wk - Age4wk
## 32 0.6156011 32 0.6258870 Age1wk - Age4wk
## 33 1.0000000 33 1.0000000 Age1wk - Age4wk
## 34 0.9171184 34 0.9342001 Age1wk - Age4wk
## 35 0.8886513 35 0.9050362 Age1wk - Age4wk
## 36 1.0000000 36 1.0000000 Age1wk - Age4wk
## 37 0.2746386 37 0.3013966 Age1wk - Age4wk
## 38 0.9353785 38 0.9539383 Age1wk - Age4wk
## 39 0.6156011 39 0.6258870 Age1wk - Age4wk
## 40 0.7801185 40 0.7954931 Age1wk - Age4wk
## 41 1.0000000 41 1.0000000 Age1wk - Age4wk
## 42 1.0000000 42 1.0000000 Age1wk - Age4wk
## 43 1.0000000 43 1.0000000 Age1wk - Age4wk
## 44 1.0000000 44 1.0000000 Age1wk - Age4wk
## 45 0.3224437 45 0.3329325 Age1wk - Age4wk
## 46 0.4267378 46 0.4364891 Age1wk - Age4wk
## 47 1.0000000 47 1.0000000 Age1wk - Age4wk
## 48 0.6156011 48 0.6258870 Age1wk - Age4wk
## 49 1.0000000 49 1.0000000 Age1wk - Age4wk
## 50 0.6156011 50 0.6258870 Age1wk - Age4wk
## 51 1.0000000 51 1.0000000 Age1wk - Age4wk
## 52 0.2508434 52 0.2714430 Age1wk - Age4wk
## 53 0.6671434 53 0.6789184 Age1wk - Age4wk
## 54 0.6156011 54 0.6258870 Age1wk - Age4wk
## 55 0.7211031 55 0.7359744 Age1wk - Age4wk
## 56 1.0000000 56 1.0000000 Age1wk - Age4wk
## 57 0.6156011 57 0.6258870 Age1wk - Age4wk
## 58 1.0000000 58 1.0000000 Age1wk - Age4wk
## 59 0.6636024 59 0.6759385 Age1wk - Age4wk
## 60 0.9806326 60 1.0000000 Age1wk - Age4wk
## 61 1.0000000 61 1.0000000 Age1wk - Age4wk
## 62 1.0000000 62 1.0000000 Age1wk - Age4wk
## 63 0.3094007 63 0.3326627 Age1wk - Age4wk
## 64 0.6156011 64 0.6258870 Age1wk - Age4wk
## 65 0.1235801 65 0.1288975 Age1wk - Age4wk
## 66 1.0000000 66 1.0000000 Age1wk - Age4wk
## 67 1.0000000 67 1.0000000 Age1wk - Age4wk
## 68 0.1477747 68 0.1615543 Age1wk - Age4wk
## 69 0.2286687 69 0.2351162 Age1wk - Age4wk
## 70 0.7207527 70 0.7317515 Age1wk - Age4wk
## 71 0.6156011 71 0.6258870 Age1wk - Age4wk
## 72 0.1954923 72 0.1997976 Age1wk - Age4wk
## 73 1.0000000 73 1.0000000 Age1wk - Age4wk
## 74 0.6671434 74 0.6789184 Age1wk - Age4wk
## 75 1.0000000 75 1.0000000 Age1wk - Age4wk
## 76 0.1425507 76 0.1493222 Age1wk - Age4wk
## 77 1.0000000 77 1.0000000 Age1wk - Age4wk
## 78 1.0000000 78 1.0000000 Age1wk - Age4wk
## 79 1.0000000 79 1.0000000 Age1wk - Age4wk
## 80 0.2070032 80 0.2129872 Age1wk - Age4wk
## 81 0.3074220 81 0.3284780 Age1wk - Age4wk
## 82 0.6156011 82 0.6258870 Age1wk - Age4wk
## 83 1.0000000 83 1.0000000 Age1wk - Age4wk
## 84 0.5681024 84 0.5741101 Age1wk - Age4wk
## 85 0.1477747 85 0.1615543 Age1wk - Age4wk
## 86 1.0000000 86 1.0000000 Age1wk - Age4wk
## 87 0.4513805 87 0.4598838 Age1wk - Age4wk
## 88 0.3224437 88 0.3329325 Age1wk - Age4wk
## 89 1.0000000 89 1.0000000 Age1wk - Age4wk
## 90 1.0000000 90 1.0000000 Age1wk - Age4wk
## 91 0.4810128 91 0.4914154 Age1wk - Age4wk
## 92 1.0000000 92 1.0000000 Age1wk - Age4wk
## 93 0.6156011 93 0.6258870 Age1wk - Age4wk
## 94 1.0000000 94 1.0000000 Age1wk - Age4wk
## 95 0.2180645 95 0.2259586 Age1wk - Age4wk
## 96 1.0000000 96 1.0000000 Age1wk - Age4wk
## 97 0.1159113 97 0.1036166 Age1wk - Age4wk
## 98 0.3224437 98 0.3329325 Age1wk - Age4wk
## 99 0.1477747 99 0.1615543 Age1wk - Age4wk
## 100 1.0000000 100 1.0000000 Age1wk - Age4wk
## 101 0.2887915 101 0.3169020 Age1wk - Age4wk
## 102 1.0000000 102 1.0000000 Age1wk - Age4wk
## 103 1.0000000 103 1.0000000 Age1wk - Age4wk
## 104 0.6156011 104 0.6258870 Age1wk - Age4wk
## 105 1.0000000 105 1.0000000 Age1wk - Age4wk
## 106 0.8799327 106 0.8945728 Age1wk - Age4wk
## 107 1.0000000 107 1.0000000 Age1wk - Age4wk
## 108 0.3694538 108 0.3808525 Age1wk - Age4wk
## 109 0.2070032 109 0.2129872 Age1wk - Age4wk
## 110 0.1477747 110 0.1615543 Age1wk - Age4wk
## 111 1.0000000 111 1.0000000 Age1wk - Age4wk
## 112 1.0000000 112 1.0000000 Age1wk - Age4wk
## 113 0.8457654 113 0.8681566 Age1wk - Age4wk
## 114 0.9358425 114 0.9566489 Age1wk - Age4wk
## 115 1.0000000 115 1.0000000 Age1wk - Age4wk
## 116 1.0000000 116 1.0000000 Age1wk - Age4wk
## 117 1.0000000 117 1.0000000 Age1wk - Age4wk
## 118 0.6156011 118 0.6258870 Age1wk - Age4wk
## 119 0.1704707 119 0.1852144 Age1wk - Age4wk
## 120 0.7154373 120 0.7306839 Age1wk - Age4wk
## 121 0.7330802 121 0.7399152 Age1wk - Age4wk
## 122 0.6156011 122 0.6258870 Age1wk - Age4wk
## 123 0.8912158 123 0.9057993 Age1wk - Age4wk
## 124 0.6156011 124 0.6258870 Age1wk - Age4wk
## 125 0.6156011 125 0.6258870 Age1wk - Age4wk
## 126 1.0000000 126 1.0000000 Age1wk - Age4wk
## 127 0.2746386 127 0.3013966 Age1wk - Age4wk
## 128 0.1159113 128 0.1200430 Age1wk - Age4wk
## 129 0.2746386 129 0.3013966 Age1wk - Age4wk
## 130 0.1704707 130 0.1865056 Age1wk - Age4wk
## 131 0.2307724 131 0.2399491 Age1wk - Age4wk
## 132 1.0000000 132 1.0000000 Age1wk - Age4wk
## 133 0.8041852 133 0.8222494 Age1wk - Age4wk
## 134 1.0000000 134 1.0000000 Age1wk - Age4wk
## 135 1.0000000 135 1.0000000 Age1wk - Age4wk
## 136 0.6214929 136 0.6344084 Age1wk - Age4wk
## 137 0.6156011 137 0.6258870 Age1wk - Age4wk
## 138 0.6156011 138 0.6258870 Age1wk - Age4wk
## 139 0.3224437 139 0.3329325 Age1wk - Age4wk
## 140 0.9820394 140 1.0000000 Age1wk - Age4wk
## 141 0.8886513 141 0.9050362 Age1wk - Age4wk
## 142 0.2746386 142 0.3013966 Age1wk - Age4wk
## 143 0.3694538 143 0.3808525 Age1wk - Age4wk
## 144 0.6156011 144 0.6258870 Age1wk - Age4wk
## 145 0.3224437 145 0.3329325 Age1wk - Age4wk
## 146 1.0000000 146 1.0000000 Age1wk - Age4wk
## 147 1.0000000 147 1.0000000 Age1wk - Age4wk
## 148 0.1159113 148 0.1200430 Age1wk - Age4wk
## 149 0.6156011 149 0.6258870 Age1wk - Age4wk
## 150 1.0000000 150 1.0000000 Age1wk - Age4wk
## 151 0.3224437 151 0.3329325 Age1wk - Age4wk
## 152 0.7113483 152 0.7222595 Age1wk - Age4wk
## 153 0.1477747 153 0.1615543 Age1wk - Age4wk
## 154 1.0000000 154 1.0000000 Age1wk - Age4wk
## 155 1.0000000 155 1.0000000 Age1wk - Age4wk
## 156 1.0000000 156 1.0000000 Age1wk - Age4wk
## 157 0.1159113 157 0.1204399 Age1wk - Age4wk
## 158 0.5293155 158 0.5362826 Age1wk - Age4wk
## 159 1.0000000 159 1.0000000 Age1wk - Age4wk
## 160 1.0000000 160 1.0000000 Age1wk - Age4wk
## 161 1.0000000 161 1.0000000 Age1wk - Age4wk
## 162 0.6156011 162 0.6258870 Age1wk - Age4wk
## 163 1.0000000 163 1.0000000 Age1wk - Age4wk
## 164 0.6888470 164 0.7004307 Age1wk - Age4wk
## 165 0.6156011 165 0.6258870 Age1wk - Age4wk
## 166 1.0000000 166 1.0000000 Age1wk - Age4wk
## 167 0.6156011 167 0.6258870 Age1wk - Age4wk
## 168 1.0000000 168 1.0000000 Age1wk - Age4wk
## 169 1.0000000 169 1.0000000 Age1wk - Age4wk
## 170 0.8799327 170 0.8945728 Age1wk - Age4wk
## 171 0.3224437 171 0.3344722 Age1wk - Age4wk
## 172 0.1159113 172 0.1046682 Age1wk - Age4wk
## 173 0.2640309 173 0.2898203 Age1wk - Age4wk
## 174 1.0000000 174 1.0000000 Age1wk - Age4wk
## 175 0.1477747 175 0.1615543 Age1wk - Age4wk
## 176 0.5018803 176 0.5068012 Age1wk - Age4wk
## 177 0.8799327 177 0.8945728 Age1wk - Age4wk
## 178 0.1159113 178 0.1036166 Age1wk - Age4wk
## 179 0.1159113 179 0.1036166 Age1wk - Age4wk
## 180 1.0000000 180 1.0000000 Age1wk - Age4wk
## 181 0.6156011 181 0.6258870 Age1wk - Age4wk
## 182 0.1689642 182 0.1844787 Age1wk - Age4wk
## 183 1.0000000 183 1.0000000 Age1wk - Age4wk
## 184 0.7218014 184 0.7362873 Age1wk - Age4wk
## 185 1.0000000 185 1.0000000 Age1wk - Age4wk
## 186 0.8041852 186 0.8222494 Age1wk - Age4wk
## 187 0.9358425 187 0.9566489 Age1wk - Age4wk
## 188 1.0000000 188 1.0000000 Age1wk - Age4wk
## 189 0.7113483 189 0.7222595 Age1wk - Age4wk
## 190 1.0000000 190 1.0000000 Age1wk - Age4wk
## 191 0.3224437 191 0.3329325 Age1wk - Age4wk
## 192 0.6156011 192 0.6258870 Age1wk - Age4wk
## 193 1.0000000 193 1.0000000 Age1wk - Age4wk
## 194 0.6156011 194 0.6258870 Age1wk - Age4wk
## 195 0.7306438 195 0.7399152 Age1wk - Age4wk
## 196 0.5018803 196 0.5073195 Age1wk - Age4wk
## 197 1.0000000 197 1.0000000 Age1wk - Age4wk
## 198 0.2508434 198 0.2714430 Age1wk - Age4wk
## 199 1.0000000 199 1.0000000 Age1wk - Age4wk
## 200 0.7677496 200 0.7784430 Age1wk - Age4wk
## 201 0.7653631 201 0.7743727 Age1wk - Age4wk
## 202 0.4267378 202 0.4364891 Age1wk - Age4wk
## 203 0.7211031 203 0.7359744 Age1wk - Age4wk
## 204 0.1704707 204 0.1852144 Age1wk - Age4wk
## 205 1.0000000 205 1.0000000 Age1wk - Age4wk
## 206 0.8799327 206 0.8945728 Age1wk - Age4wk
## 207 0.6156011 207 0.6258870 Age1wk - Age4wk
## 208 0.4246945 208 0.4349506 Age1wk - Age4wk
## 209 0.7544636 209 0.7625185 Age1wk - Age4wk
## 210 1.0000000 210 1.0000000 Age1wk - Age4wk
## 211 0.3094772 211 0.3329325 Age1wk - Age4wk
## 212 1.0000000 212 1.0000000 Age1wk - Age4wk
## 213 1.0000000 213 1.0000000 Age1wk - Age4wk
## 214 0.2180645 214 0.2259586 Age1wk - Age4wk
## 215 0.2746386 215 0.3013966 Age1wk - Age4wk
## 216 0.6432889 216 0.6564839 Age1wk - Age4wk
## 217 0.4888055 217 0.4977142 Age1wk - Age4wk
## 218 1.0000000 218 1.0000000 Age1wk - Age4wk
## 219 0.3224437 219 0.3329325 Age1wk - Age4wk
## 220 0.4499688 220 0.4598838 Age1wk - Age4wk
## 221 0.6156011 221 0.6258870 Age1wk - Age4wk
## 222 1.0000000 222 1.0000000 Age1wk - Age4wk
## 223 1.0000000 223 1.0000000 Age1wk - Age4wk
## 224 1.0000000 224 1.0000000 Age1wk - Age4wk
## 225 1.0000000 225 1.0000000 Age1wk - Age4wk
## 226 0.2746386 226 0.3013966 Age1wk - Age4wk
## 227 1.0000000 227 1.0000000 Age1wk - Age4wk
## 228 0.4539053 228 0.4613240 Age1wk - Age4wk
## 229 1.0000000 229 1.0000000 Age1wk - Age4wk
## 230 1.0000000 230 1.0000000 Age1wk - Age4wk
## 231 0.4967285 231 0.4993197 Age1wk - Age4wk
## 232 0.2746386 232 0.3013966 Age1wk - Age4wk
## 233 0.6156011 233 0.6258870 Age1wk - Age4wk
## 234 1.0000000 234 1.0000000 Age1wk - Age4wk
## 235 0.2746386 235 0.3013966 Age1wk - Age4wk
## 236 1.0000000 236 1.0000000 Age1wk - Age4wk
## 237 0.3694538 237 0.3808525 Age1wk - Age4wk
## 238 0.9358425 238 0.9566489 Age1wk - Age4wk
## 239 0.7801185 239 0.7954931 Age1wk - Age4wk
## 240 1.0000000 240 1.0000000 Age1wk - Age4wk
## 241 1.0000000 241 1.0000000 Age1wk - Age4wk
## 242 0.1159113 242 0.1036166 Age1wk - Age4wk
## 243 1.0000000 243 1.0000000 Age1wk - Age4wk
## 244 1.0000000 244 1.0000000 Age1wk - Age4wk
## 245 0.2508434 245 0.2714430 Age1wk - Age4wk
## 246 1.0000000 246 1.0000000 Age1wk - Age4wk
## 247 0.1765727 247 0.1877824 Age1wk - Age4wk
## 248 0.1028244 248 0.1036166 Age1wk - Age4wk
## 249 0.3224437 249 0.3329325 Age1wk - Age4wk
## 250 1.0000000 250 1.0000000 Age1wk - Age4wk
## 251 1.0000000 251 1.0000000 Age1wk - Age4wk
## 252 0.4513805 252 0.4598838 Age1wk - Age4wk
## 253 0.9820394 253 1.0000000 Age1wk - Age4wk
## 254 0.1816424 254 0.1877824 Age1wk - Age4wk
## 255 0.1159113 255 0.1046682 Age1wk - Age4wk
## 256 1.0000000 256 1.0000000 Age1wk - Age4wk
## 257 1.0000000 257 1.0000000 Age1wk - Age4wk
## 258 0.6214929 258 0.6344084 Age1wk - Age4wk
## 259 0.9941052 259 1.0000000 Age1wk - Age4wk
## 260 1.0000000 260 1.0000000 Age1wk - Age4wk
## 261 0.6156011 261 0.6258870 Age1wk - Age4wk
## 262 1.0000000 262 1.0000000 Age1wk - Age4wk
## 263 0.7207527 263 0.7317515 Age1wk - Age4wk
## 264 1.0000000 264 1.0000000 Age1wk - Age4wk
## 265 0.2746386 265 0.3013966 Age1wk - Age4wk
## 266 1.0000000 266 1.0000000 Age1wk - Age4wk
## 267 0.9820394 267 1.0000000 Age1wk - Age4wk
## 268 0.2508434 268 0.2714430 Age1wk - Age4wk
## 269 1.0000000 269 1.0000000 Age1wk - Age4wk
## 270 0.8907850 270 0.9057715 Age1wk - Age4wk
## 271 0.4218229 271 0.4323511 Age1wk - Age4wk
## 272 0.6156011 272 0.6258870 Age1wk - Age4wk
## 273 0.2746386 273 0.3013966 Age1wk - Age4wk
## 274 0.6481130 274 0.6616225 Age1wk - Age4wk
## 275 0.2378919 275 0.2478953 Age1wk - Age4wk
## 276 0.1235801 276 0.1288975 Age1wk - Age4wk
## 277 0.2508434 277 0.2714430 Age1wk - Age4wk
## 278 0.2508434 278 0.2714430 Age1wk - Age4wk
## 279 1.0000000 279 1.0000000 Age1wk - Age4wk
## 280 0.3224437 280 0.3329325 Age1wk - Age4wk
## 281 0.3224437 281 0.3329325 Age1wk - Age4wk
## 282 1.0000000 282 1.0000000 Age1wk - Age4wk
## 283 0.1159113 283 0.1204399 Age1wk - Age4wk
## 284 0.2287792 284 0.2356633 Age1wk - Age4wk
## 285 0.3224437 285 0.3329325 Age1wk - Age4wk
## 286 0.7306438 286 0.7399152 Age1wk - Age4wk
## 287 0.9353785 287 0.9539383 Age1wk - Age4wk
## 288 1.0000000 288 1.0000000 Age1wk - Age4wk
## 289 1.0000000 289 1.0000000 Age1wk - Age4wk
## 290 0.5979575 290 0.6063418 Age1wk - Age4wk
## 291 0.2746386 291 0.3013966 Age1wk - Age4wk
## 292 1.0000000 292 1.0000000 Age1wk - Age4wk
## 293 0.6156011 293 0.6258870 Age1wk - Age4wk
## 294 0.6106036 294 0.6178069 Age1wk - Age4wk
## 295 1.0000000 295 1.0000000 Age1wk - Age4wk
## 296 1.0000000 296 1.0000000 Age1wk - Age4wk
## 297 1.0000000 297 1.0000000 Age1wk - Age4wk
## 298 0.2963575 298 0.3169020 Age1wk - Age4wk
## 299 1.0000000 299 1.0000000 Age1wk - Age4wk
## 300 1.0000000 300 1.0000000 Age1wk - Age4wk
## 301 0.4532870 301 0.4599598 Age1wk - Age4wk
## 302 0.6310966 302 0.6462709 Age1wk - Age4wk
## 303 0.6156011 303 0.6258870 Age1wk - Age4wk
## 304 0.1704707 304 0.1865056 Age1wk - Age4wk
## 305 1.0000000 305 1.0000000 Age1wk - Age4wk
## 306 0.8907850 306 0.9057715 Age1wk - Age4wk
## 307 0.2746386 307 0.3013966 Age1wk - Age4wk
## 308 0.2093308 308 0.2178862 Age1wk - Age4wk
## 309 1.0000000 309 1.0000000 Age1wk - Age4wk
## 310 0.3094772 310 0.3329325 Age1wk - Age4wk
## 311 0.2746386 311 0.3013966 Age1wk - Age4wk
## 312 0.1159113 312 0.1200430 Age1wk - Age4wk
## 313 1.0000000 313 1.0000000 Age1wk - Age4wk
## 314 0.3507103 314 0.3627825 Age1wk - Age4wk
## 315 0.9353785 315 0.9539383 Age1wk - Age4wk
## 316 0.9353785 316 0.9539383 Age1wk - Age4wk
## 317 0.9353785 317 0.9539383 Age1wk - Age4wk
## 318 0.5293155 318 0.5362826 Age1wk - Age4wk
## 319 1.0000000 319 1.0000000 Age1wk - Age4wk
## 320 1.0000000 320 1.0000000 Age1wk - Age4wk
## 321 1.0000000 321 1.0000000 Age1wk - Age4wk
## 322 0.9820394 322 1.0000000 Age1wk - Age4wk
## 323 0.1704707 323 0.1852144 Age1wk - Age4wk
## 324 0.9771507 324 1.0000000 Age1wk - Age4wk
## 325 1.0000000 325 1.0000000 Age1wk - Age4wk
## 326 0.7519977 326 0.7573074 Age1wk - Age4wk
## 327 0.7133253 327 0.7260649 Age1wk - Age4wk
## 328 0.3224437 328 0.3329325 Age1wk - Age4wk
## 329 0.2070032 329 0.2129872 Age1wk - Age4wk
## 330 1.0000000 330 1.0000000 Age1wk - Age4wk
## 331 1.0000000 331 1.0000000 Age1wk - Age4wk
## 332 0.9171184 332 0.9342001 Age1wk - Age4wk
## 333 0.8799327 333 0.8945728 Age1wk - Age4wk
## 334 0.1974004 334 0.2033831 Age1wk - Age4wk
## 335 0.4146536 335 0.4288112 Age1wk - Age4wk
## 336 0.5688616 336 0.5741101 Age1wk - Age4wk
## 337 0.8799327 337 0.8945728 Age1wk - Age4wk
## 338 0.2746386 338 0.3013966 Age1wk - Age4wk
## 339 0.6156011 339 0.6258870 Age1wk - Age4wk
## 340 0.2640309 340 0.2898203 Age1wk - Age4wk
## 341 1.0000000 341 1.0000000 Age1wk - Age4wk
## 342 0.6432889 342 0.6564839 Age1wk - Age4wk
## 343 0.8496096 343 0.8681566 Age1wk - Age4wk
## PValue_adj_withinNhood
## 1 0.7244973681
## 2 0.3968267906
## 3 0.7741359491
## 4 0.0420293274
## 5 0.0386138100
## 6 0.2708395280
## 7 0.0639943505
## 8 0.2211852757
## 9 0.9953704028
## 10 0.0062405123
## 11 0.8919487757
## 12 0.2678406963
## 13 0.0374681945
## 14 0.5748068106
## 15 0.7733500363
## 16 0.2765532447
## 17 0.9912076227
## 18 1.0000000000
## 19 0.2853819816
## 20 0.0353502325
## 21 0.0869404181
## 22 0.0524834302
## 23 0.7171302338
## 24 0.0108428632
## 25 0.1720370671
## 26 0.0091477149
## 27 0.9780272498
## 28 0.6036414471
## 29 0.9767181269
## 30 0.6863646865
## 31 0.4557169773
## 32 0.2523568330
## 33 0.8318362578
## 34 0.5448439125
## 35 0.5137949331
## 36 1.0000000000
## 37 0.0560797826
## 38 0.5697776543
## 39 0.2693758914
## 40 0.4230380362
## 41 0.8356781395
## 42 0.8555512418
## 43 0.9780272575
## 44 0.6847558982
## 45 0.0787437793
## 46 0.1269016175
## 47 1.0000000000
## 48 0.2769966488
## 49 1.0000000000
## 50 0.2692388196
## 51 0.7423692419
## 52 0.0378415327
## 53 0.3228740661
## 54 0.2327080509
## 55 0.3679097488
## 56 0.9835147909
## 57 0.2678944184
## 58 0.7549199073
## 59 0.3172909656
## 60 0.6175412149
## 61 0.9347211625
## 62 1.0000000000
## 63 0.0685552560
## 64 0.2678944184
## 65 0.0049759791
## 66 1.0000000000
## 67 0.9864414893
## 68 0.0081150618
## 69 0.0273335816
## 70 0.3635283273
## 71 0.2799818373
## 72 0.0188082991
## 73 1.0000000000
## 74 0.3224059266
## 75 1.0000000000
## 76 0.0066495952
## 77 1.0000000000
## 78 0.7681741709
## 79 0.8426973727
## 80 0.0223297923
## 81 0.0672205614
## 82 0.2765359354
## 83 1.0000000000
## 84 0.1921279246
## 85 0.0088142054
## 86 1.0000000000
## 87 0.1381776906
## 88 0.0847391255
## 89 0.9505375356
## 90 1.0000000000
## 91 0.1514559101
## 92 0.6518187452
## 93 0.2477785104
## 94 0.7687688689
## 95 0.0251016854
## 96 0.9321306865
## 97 0.0012335734
## 98 0.0743393180
## 99 0.0074947403
## 100 1.0000000000
## 101 0.0606209534
## 102 1.0000000000
## 103 1.0000000000
## 104 0.2332839513
## 105 1.0000000000
## 106 0.5022470897
## 107 0.6716119050
## 108 0.1035862918
## 109 0.0218891903
## 110 0.0096162420
## 111 0.8762435723
## 112 0.9542238290
## 113 0.4684998110
## 114 0.5811499827
## 115 1.0000000000
## 116 0.8647793384
## 117 1.0000000000
## 118 0.2552217491
## 119 0.0141438691
## 120 0.3566757461
## 121 0.3825695460
## 122 0.2416906375
## 123 0.5248559278
## 124 0.2405395627
## 125 0.2387311787
## 126 1.0000000000
## 127 0.0481546893
## 128 0.0034464866
## 129 0.0542747207
## 130 0.0149099714
## 131 0.0289306568
## 132 1.0000000000
## 133 0.4394067523
## 134 0.9348376806
## 135 1.0000000000
## 136 0.2880973078
## 137 0.2775565213
## 138 0.2678944176
## 139 0.0815501153
## 140 0.6221728371
## 141 0.5155731990
## 142 0.0509634212
## 143 0.1044811113
## 144 0.2796696834
## 145 0.0854737563
## 146 0.7254413918
## 147 0.7410109769
## 148 0.0032803505
## 149 0.2678944172
## 150 0.9987166236
## 151 0.0856526837
## 152 0.3500195087
## 153 0.0099090918
## 154 1.0000000000
## 155 1.0000000000
## 156 0.7546866450
## 157 0.0040552053
## 158 0.1763041664
## 159 0.6876450759
## 160 0.9355393360
## 161 1.0000000000
## 162 0.2678944183
## 163 0.9140711029
## 164 0.3353861575
## 165 0.2717592080
## 166 0.8943543371
## 167 0.2247036814
## 168 0.9801589808
## 169 1.0000000000
## 170 0.4982380164
## 171 0.0874264151
## 172 0.0025300269
## 173 0.0431070809
## 174 1.0000000000
## 175 0.0096023485
## 176 0.1625045704
## 177 0.5013966180
## 178 0.0008879162
## 179 0.0017078414
## 180 0.9143431418
## 181 0.2678944184
## 182 0.0123151771
## 183 0.8123749416
## 184 0.3703703880
## 185 1.0000000000
## 186 0.4407778678
## 187 0.5802910091
## 188 1.0000000000
## 189 0.3504893744
## 190 0.8356991819
## 191 0.0815338398
## 192 0.2468673438
## 193 0.8367360063
## 194 0.2192937441
## 195 0.3791679049
## 196 0.1638792936
## 197 1.0000000000
## 198 0.0346896585
## 199 1.0000000000
## 200 0.4118540236
## 201 0.4083423957
## 202 0.1264269397
## 203 0.3677518407
## 204 0.0131020605
## 205 1.0000000000
## 206 0.4951329656
## 207 0.2707529850
## 208 0.1238176360
## 209 0.4003276345
## 210 0.6911559990
## 211 0.0703767388
## 212 0.8408614922
## 213 0.8658726458
## 214 0.0254302673
## 215 0.0538839436
## 216 0.3037334699
## 217 0.1553346859
## 218 0.8801290437
## 219 0.0856947784
## 220 0.1351218277
## 221 0.2788506707
## 222 0.7457915157
## 223 1.0000000000
## 224 1.0000000000
## 225 1.0000000000
## 226 0.0568493799
## 227 0.9618655201
## 228 0.1415972887
## 229 1.0000000000
## 230 0.9400285969
## 231 0.1593006943
## 232 0.0543494965
## 233 0.2681124255
## 234 1.0000000000
## 235 0.0566716255
## 236 0.7093706698
## 237 0.1035824867
## 238 0.5792043308
## 239 0.4228477645
## 240 0.8321666153
## 241 0.6817446313
## 242 0.0016713512
## 243 1.0000000000
## 244 1.0000000000
## 245 0.0378535621
## 246 1.0000000000
## 247 0.0159584625
## 248 0.0002997796
## 249 0.0813590526
## 250 0.7668840292
## 251 1.0000000000
## 252 0.1376332700
## 253 0.6298794729
## 254 0.0169462337
## 255 0.0021875590
## 256 1.0000000000
## 257 0.6559288634
## 258 0.2872391837
## 259 0.6405167911
## 260 1.0000000000
## 261 0.2332105986
## 262 1.0000000000
## 263 0.3624319322
## 264 0.8826813597
## 265 0.0548379526
## 266 1.0000000000
## 267 0.6275263634
## 268 0.0387600615
## 269 0.7352326442
## 270 0.5219193511
## 271 0.1217506264
## 272 0.2518806094
## 273 0.0556232024
## 274 0.3079954004
## 275 0.0305167441
## 276 0.0050440877
## 277 0.0375801809
## 278 0.0354924259
## 279 0.9817631196
## 280 0.0793470892
## 281 0.0805289751
## 282 1.0000000000
## 283 0.0038393892
## 284 0.0280137814
## 285 0.0773361395
## 286 0.3778629412
## 287 0.5641216667
## 288 0.7703955531
## 289 1.0000000000
## 290 0.2057113418
## 291 0.0508021624
## 292 1.0000000000
## 293 0.2678944522
## 294 0.2118420747
## 295 0.8764315958
## 296 0.6630622496
## 297 0.6821124376
## 298 0.0630731786
## 299 0.9063559887
## 300 0.6590283795
## 301 0.1400828630
## 302 0.2943891056
## 303 0.2766243060
## 304 0.0147807938
## 305 0.7462288525
## 306 0.5220052115
## 307 0.0547211060
## 308 0.0231911638
## 309 0.8612987134
## 310 0.0699115942
## 311 0.0548046199
## 312 0.0035175493
## 313 1.0000000000
## 314 0.0961130385
## 315 0.5615543744
## 316 0.5667175268
## 317 0.5699536374
## 318 0.1774672880
## 319 1.0000000000
## 320 0.8378557986
## 321 1.0000000000
## 322 0.6287128477
## 323 0.0137622123
## 324 0.6124996870
## 325 0.9453417300
## 326 0.3958274007
## 327 0.3535431364
## 328 0.0829187826
## 329 0.0217729794
## 330 0.8087083603
## 331 0.7638926936
## 332 0.5454581853
## 333 0.5046102345
## 334 0.0195673894
## 335 0.1184724660
## 336 0.1940431771
## 337 0.5053840991
## 338 0.0469469688
## 339 0.2193689719
## 340 0.0429491365
## 341 0.8385667366
## 342 0.3038273979
## 343 0.4731062196
##
## $design_df
## Sample Age
## 1_1wk 1_1wk 1wk
## 1_4wk 1_4wk 4wk
## 1_16wk 1_16wk 16wk
## 1_32wk 1_32wk 32wk
## 1_52wk 1_52wk 52wk
## 2_32wk 2_32wk 32wk
## 2_4wk 2_4wk 4wk
## 2_1wk 2_1wk 1wk
## 2_16wk 2_16wk 16wk
## 2_52wk 2_52wk 52wk
## 3_4wk 3_4wk 4wk
## 3_1wk 3_1wk 1wk
## 3_52wk 3_52wk 52wk
## 3_16wk 3_16wk 16wk
## 3_32wk 3_32wk 32wk
## 4_1wk 4_1wk 1wk
## 4_16wk 4_16wk 16wk
## 4_4wk 4_4wk 4wk
## 4_32wk 4_32wk 32wk
## 4_52wk 4_52wk 52wk
## 5_32wk 5_32wk 32wk
## 5_52wk 5_52wk 52wk
## 5_1wk 5_1wk 1wk
## 5_4wk 5_4wk 4wk
## 5_16wk 5_16wk 16wk
##
## $formula
## [1] "~0 + Age"
##
## $contrasts
## [1] "Age1wk - Age4wk"15.3 Multi-contrast testing
Use per_contrast = FALSE to fit one model and test multiple contrasts jointly. Use per_contrast = TRUE to run each contrast and stack results.
contrasts <- c(
"Age1wk - Age4wk",
"Age4wk - Age16wk",
"Age16wk - Age32wk",
"Age32wk - Age52wk"
)
res2 <- RunMilo(
sce = sce,
sample_col = "Sample",
condition_col = "Age",
name = "milo_multi",
contrasts = contrasts,
per_contrast = TRUE,
k1 = 11, k2 = 11, d1 = 40, d2 = 40, d3 = 40,
prop = 0.2,
refinement_scheme = "graph"
)
head(res2$da_results)## logFC logCPM F PValue FDR Nhood
## 1 -0.4248810 13.66075 0.12423442 0.72449737 1.0000000 1
## 2 -1.1178226 13.37924 0.71801065 0.39682679 0.7519977 2
## 3 0.3680766 13.57295 0.08235778 0.77413595 1.0000000 3
## 4 -2.8623635 13.87550 4.13557017 0.04202933 0.2640309 4
## 5 -2.8294618 13.65808 4.27942341 0.03861381 0.2508434 5
## 6 -1.4177180 13.55053 1.21268563 0.27083953 0.6156011 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 1.0000000 Age1wk - Age4wk 0.8527620
## 2 0.7573074 Age1wk - Age4wk 0.7936536
## 3 1.0000000 Age1wk - Age4wk 0.8723942
## 4 0.2898203 Age1wk - Age4wk 0.1681173
## 5 0.2714430 Age1wk - Age4wk 0.1544552
## 6 0.6258870 Age1wk - Age4wk 0.894818115.4 GLMM (random intercept)
When samples are not independent (e.g., repeated measures), a random intercept can help control correlation structure.
library(scRNAseq)
library(scater)
library(scran)
library(scuttle)
library(sclet)
sce2 <- KotliarovPBMCData(mode = "rna", ensembl = FALSE)colData(sce2)$ObsID <- paste(colData(sce2)$tenx_lane, colData(sce2)$sampleid, sep = "_")
set.seed(42)
keep_samps <- sample(unique(colData(sce2)$ObsID), size = 40)
sce2 <- sce2[, colData(sce2)$ObsID %in% keep_samps]
sce2 <- NormalizeData(sce2)
sce2 <- RunPCA(sce2, ncomponents = 30)
sce2 <- RunUMAP(sce2, dims = 1:30)
res3 <- RunMilo(
sce = sce2,
sample_col = "ObsID",
condition_col = "adjmfc.time",
name = "milo_glmm",
contrasts = c("adjmfc.timed0 high"),
glmm = TRUE,
random_effect = "tenx_lane",
k1 = 60, k2 = 60, d1 = 30, d2 = 30, d3 = 30,
prop = 0.05,
overlap = 25
)
head(res3$da_results)## logFC logCPM SE tvalue PValue
## 1 1.19426566 11.11520 0.3418064 3.49398244 0.0004796897
## 2 -0.56190987 10.58540 0.3579033 -1.57000457 0.1164654238
## 3 -0.03096640 12.08108 0.3685682 -0.08401811 0.9330451923
## 4 -1.37537254 10.56466 0.4344745 -3.16560037 0.0015507645
## 5 0.04402348 11.02846 0.3081513 0.14286319 0.8864021928
## 6 0.35057452 11.89417 0.3564932 0.98339738 0.3254452341
## tenx_lane_variance Converged Logliklihood Nhood
## 1 0.00000001 TRUE 337.2157 1
## 2 0.01554443 FALSE 200.8052 2
## 3 0.00000001 TRUE 850.5412 3
## 4 1.12729627 TRUE 242.8243 4
## 5 0.00000001 TRUE 238.1128 5
## 6 0.09303859 TRUE 776.1802 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 0.003662778 adjmfc.timed0 high 0.0004796897
## 2 0.258102408 adjmfc.timed0 high 0.1164654238
## 3 0.959870868 adjmfc.timed0 high 0.9330451923
## 4 0.010496151 adjmfc.timed0 high 0.0015507645
## 5 0.930141991 adjmfc.timed0 high 0.8864021928
## 6 0.501574206 adjmfc.timed0 high 0.325445234115.5 Refit after dropping separated neighbourhoods
In GLMM mode, some neighbourhoods can show perfect separation and return unstable estimates. You can diagnose with miloR::checkSeparation() and refit after dropping those neighbourhoods.
If you keep multiple Milo runs in the same object, give them different name values and inspect a specific record with get_milo(sce, id = "your_id").
milo_info <- get_milo(res3$sce)
design_df <- milo_info$design_df
bad_hood <- which(miloR::checkSeparation(
res3$milo,
design.df = design_df,
condition = "adjmfc.time",
min.val = 10
))
refit <- refit_milo(
milo = res3$milo,
design_df = design_df,
bad_hood = bad_hood,
formula = milo_info$formula,
contrasts = milo_info$contrasts,
glmm = TRUE,
old_results = res3$da_results
)
head(refit$da_clean)## logFC logCPM SE tvalue PValue
## 1 1.19429868 11.11520 0.3367312 3.54674144 0.0003932523
## 2 -0.55843100 10.58540 0.3533867 -1.58022638 0.1141037734
## 3 -0.03091596 12.08108 0.3724387 -0.08300952 0.9338471512
## 4 -1.38041314 10.56466 0.4292965 -3.21552358 0.0013046943
## 5 0.04402347 11.02846 0.3081513 0.14286317 0.8864022129
## 6 0.35927884 11.89417 0.3608347 0.99568829 0.3194374891
## tenx_lane_variance Converged Logliklihood Nhood
## 1 0.00000001 TRUE 337.0783 1
## 2 0.02435859 FALSE 201.1274 2
## 3 0.00000001 TRUE 850.5142 3
## 4 1.15081208 TRUE 243.4212 4
## 5 0.00000001 TRUE 238.1128 5
## 6 0.08049940 TRUE 776.0125 6
## SpatialFDR
## 1 0.003083938
## 2 0.257815506
## 3 0.959598427
## 4 0.008830656
## 5 0.928652487
## 6 0.492991000