22 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.
22.1 Requirements
Before running Milo DA, prepare a SingleCellExperiment with:
reducedDims(sce)$PCAcolData(sce)containing a sample column and a condition column
UMAP is optional (used for visualization only).
22.2 Two-group DA (GLM)
library(MouseThymusAgeing)
library(scater)
library(sclet)
sce <- MouseSMARTseqData()
colData(sce)$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
## 339## logFC logCPM F PValue FDR Nhood
## 1 0.3089824 13.77764 0.06225506 0.80297414 1.0000000 1
## 2 -1.9061370 13.49367 1.88177693 0.17017772 0.5016543 2
## 3 0.1589225 13.62763 0.01202260 0.91269209 1.0000000 3
## 4 -0.9256544 13.61763 0.37873529 0.54660693 0.8515624 4
## 5 -3.2415458 13.78463 4.95133825 0.02610325 0.2047089 5
## 6 -1.8640128 13.78308 1.82853346 0.17634597 0.5069113 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 1.0000000 Age1wk - Age4wk 0.80297414
## 2 0.5174654 Age1wk - Age4wk 0.17017772
## 3 1.0000000 Age1wk - Age4wk 0.91269209
## 4 0.8711589 Age1wk - Age4wk 0.54660693
## 5 0.2108180 Age1wk - Age4wk 0.02610325
## 6 0.5246127 Age1wk - Age4wk 0.17634597## $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 0.30898235 13.77764 6.225506e-02 0.8029741404
## 2 -1.90613696 13.49367 1.881777e+00 0.1701777150
## 3 0.15892253 13.62763 1.202260e-02 0.9126920869
## 4 -0.92565436 13.61763 3.787353e-01 0.5466069277
## 5 -3.24154575 13.78463 4.951338e+00 0.0261032547
## 6 -1.86401277 13.78308 1.828533e+00 0.1763459652
## 7 1.06238803 13.71063 6.704197e-01 0.4129340959
## 8 -3.07214014 13.52167 4.656772e+00 0.0309662914
## 9 -0.05716276 13.47313 2.174914e-03 0.9628047372
## 10 -4.31005125 13.49738 8.408827e+00 0.0037460282
## 11 -0.58583386 13.49193 1.932042e-01 0.6602771084
## 12 -1.54697794 13.54854 1.373925e+00 0.2411799146
## 13 -0.62548534 13.61055 2.343423e-01 0.6283382054
## 14 -0.87364340 13.53510 4.482993e-01 0.5031664984
## 15 -0.31413049 13.74724 6.226893e-02 0.8029526548
## 16 0.00000000 13.53958 0.000000e+00 1.0000000000
## 17 -0.17357626 13.52712 1.867442e-02 0.8913080527
## 18 -1.87498088 13.67509 2.218369e+00 0.1364235529
## 19 1.18534653 13.58368 8.821441e-01 0.3476485575
## 20 1.73680048 13.64883 1.694486e+00 0.1930549120
## 21 3.76710384 13.63423 6.614807e+00 0.0101345317
## 22 -1.87544506 13.62591 2.284000e+00 0.1307609999
## 23 -0.61148315 13.40594 2.211956e-01 0.6381455557
## 24 -2.57488554 13.73203 3.048506e+00 0.0808567355
## 25 -3.80125603 13.66222 6.517674e+00 0.0107024688
## 26 0.71282463 13.64547 3.014664e-01 0.5829826331
## 27 -0.78187675 13.71333 3.616482e-01 0.5476124188
## 28 1.89913751 13.75141 2.087737e+00 0.1485320987
## 29 -1.84011337 13.69283 1.532680e+00 0.2157535073
## 30 -1.03728143 13.84318 6.666794e-01 0.4142404126
## 31 0.11485914 13.98842 9.353034e-03 0.9229586931
## 32 -2.34166108 13.90132 2.732656e+00 0.0983619652
## 33 0.67985803 13.83413 3.056155e-01 0.5804014350
## 34 -1.06136849 13.89741 6.718173e-01 0.4124475447
## 35 -1.66143087 13.69066 1.552877e+00 0.2351135572
## 36 -4.13384976 13.71524 7.365245e+00 0.0066664655
## 37 -0.85205264 13.51053 4.133111e-01 0.5203154060
## 38 -1.21338675 13.71454 5.688156e-01 0.4507561369
## 39 0.08621122 13.95960 4.744686e-03 0.9450858318
## 40 1.21039289 13.57501 8.502911e-01 0.3565028212
## 41 -1.87631286 13.57379 1.808834e+00 0.1786931909
## 42 -0.85478210 13.49017 4.186244e-01 0.5176461348
## 43 0.01465867 13.44670 1.193011e-04 0.9912855978
## 44 -3.62386677 13.45089 6.523401e+00 0.0106680936
## 45 -3.27942632 13.86024 5.121236e+00 0.0236662735
## 46 0.00000000 13.68601 0.000000e+00 1.0000000000
## 47 -1.65870438 13.56415 1.659694e+00 0.2351135572
## 48 0.00000000 13.51161 0.000000e+00 1.0000000000
## 49 0.16879868 13.78403 1.813737e-02 0.8928727963
## 50 -4.54499493 13.93165 8.879910e+00 0.0028934850
## 51 -1.72881523 13.67884 1.579732e+00 0.2088426439
## 52 -2.99117604 13.55100 4.704744e+00 0.0301141308
## 53 0.73513127 13.54483 3.395986e-01 0.5600804138
## 54 -0.48464491 13.46330 1.449680e-01 0.7034031768
## 55 -1.31566023 13.52143 1.393066e+00 0.2379293712
## 56 -0.40706079 13.40735 9.838895e-02 0.7537812400
## 57 0.56941687 13.47965 1.891931e-01 0.6636028946
## 58 0.10734614 13.95586 8.329844e-03 0.9272823590
## 59 -1.07940089 13.60238 6.673969e-01 0.4139893461
## 60 -0.32011331 13.44084 6.370998e-02 0.8007330886
## 61 0.00000000 13.68436 0.000000e+00 1.0000000000
## 62 -1.31557447 13.45526 1.431467e+00 0.2351135279
## 63 -3.77870434 13.64829 6.519140e+00 0.0106936618
## 64 0.00000000 13.50328 0.000000e+00 1.0000000000
## 65 -0.30830967 13.88128 5.921923e-02 0.8077416187
## 66 -4.39687316 13.71923 8.150628e+00 0.0043176902
## 67 -1.25109619 13.63437 7.790596e-01 0.3774601841
## 68 -1.41187505 13.44026 1.085928e+00 0.2974122653
## 69 2.56514727 13.46614 3.647819e+00 0.0561848343
## 70 0.00000000 13.64507 0.000000e+00 1.0000000000
## 71 -1.88872886 13.51332 2.012863e+00 0.1560166642
## 72 0.00000000 13.38681 0.000000e+00 1.0000000000
## 73 -0.96654043 13.60197 5.422483e-01 0.4615279288
## 74 0.00000000 13.71862 0.000000e+00 1.0000000000
## 75 0.16277509 13.61710 1.698348e-02 0.8963165707
## 76 -0.69648377 13.87234 3.221242e-01 0.5703526514
## 77 -3.37078919 13.61016 5.338709e+00 0.0208867779
## 78 -3.22936219 13.58885 5.038461e+00 0.0248226150
## 79 -2.42722965 13.66979 3.194005e+00 0.0739533680
## 80 -1.31543074 13.63071 1.358819e+00 0.2437832428
## 81 -1.87717763 13.80478 1.827679e+00 0.1764470127
## 82 0.00000000 13.58349 0.000000e+00 1.0000000000
## 83 0.00000000 13.62845 0.000000e+00 1.0000000000
## 84 0.00000000 13.53978 0.000000e+00 1.0000000000
## 85 -0.07191857 13.44069 3.452649e-03 0.9531456025
## 86 0.00000000 13.59596 0.000000e+00 1.0000000000
## 87 1.99703003 13.58198 2.349067e+00 0.1254046574
## 88 0.55439741 13.66428 1.845895e-01 0.6674720859
## 89 1.22419294 13.64753 8.827053e-01 0.3474952582
## 90 -3.85981770 13.55334 7.087596e+00 0.0077802493
## 91 -1.31566847 13.58517 1.395095e+00 0.2375879109
## 92 4.76235760 13.50817 9.965458e+00 0.0016020348
## 93 -1.99688181 13.66296 2.387855e+00 0.1223279929
## 94 2.91666287 13.41743 4.528832e+00 0.0333643289
## 95 -0.44269116 13.54200 1.243254e-01 0.7244007264
## 96 2.01599814 13.51948 2.312440e+00 0.1283890921
## 97 -3.26906121 13.53785 5.391008e+00 0.0202702592
## 98 1.72594265 13.63702 2.064652e+00 0.1507955240
## 99 -1.47202418 13.66303 1.119454e+00 0.2900737553
## 100 2.22320707 13.45012 2.759727e+00 0.0967109783
## 101 0.00000000 13.43539 0.000000e+00 1.0000000000
## 102 0.00000000 13.50409 0.000000e+00 1.0000000000
## 103 -1.74832915 13.81033 1.754306e+00 0.1853810060
## 104 -1.31579799 13.71033 7.821877e-01 0.3765042513
## 105 -2.36688818 13.53328 2.868302e+00 0.0903860628
## 106 0.43885833 13.55685 1.217118e-01 0.7271960990
## 107 -0.14745731 13.81156 1.466265e-02 0.9036237895
## 108 -3.49895858 13.55544 6.015744e+00 0.0142038138
## 109 -3.26288360 13.52032 5.205298e+00 0.0225490113
## 110 0.10161259 13.68506 6.186252e-03 0.9565571570
## 111 -2.58094758 13.43912 3.488393e+00 0.0618436715
## 112 -0.57776211 13.68886 1.818066e-01 0.6698387990
## 113 0.43808689 13.51600 1.140614e-01 0.7355772826
## 114 1.71957217 13.76278 1.785335e+00 0.1815403798
## 115 -0.85526212 13.59583 4.411022e-01 0.5066135176
## 116 -2.57412262 13.74069 3.190518e+00 0.0741112335
## 117 0.00000000 13.49479 0.000000e+00 1.0000000000
## 118 0.65636076 13.61012 2.522969e-01 0.6154787220
## 119 0.00000000 13.51832 0.000000e+00 1.0000000000
## 120 -2.57592246 13.42295 3.465731e+00 0.0626960392
## 121 1.05547040 13.52387 6.915930e-01 0.4056523573
## 122 -1.13741989 13.78688 7.138520e-01 0.3981978265
## 123 -1.53977902 13.45767 1.325172e+00 0.2497066194
## 124 -0.13789659 13.47804 5.809151e-03 0.9392480811
## 125 -3.94764725 13.39424 7.897700e+00 0.0049639617
## 126 -2.20652700 14.13848 2.368394e+00 0.1238610372
## 127 2.46901875 13.51993 3.281027e+00 0.0701293072
## 128 4.56302252 13.45845 9.475418e+00 0.0020907528
## 129 -3.20468825 13.56003 5.248073e+00 0.0220016304
## 130 -1.24873513 13.54404 1.350427e+00 0.2452443336
## 131 -0.43051228 13.42631 1.194871e-01 0.7296021134
## 132 0.00000000 13.63423 0.000000e+00 1.0000000000
## 133 -0.17286653 13.74265 1.875158e-02 0.8910851234
## 134 0.12891467 13.50509 1.105622e-02 0.9162610435
## 135 0.00000000 14.04518 0.000000e+00 1.0000000000
## 136 -1.00100355 13.43201 5.794680e-01 0.4465474065
## 137 -1.42273680 13.56908 1.117403e+00 0.2905160106
## 138 -1.94625441 13.73399 2.285606e+00 0.1306257396
## 139 0.00000000 13.55136 0.000000e+00 1.0000000000
## 140 0.03804163 13.56195 4.575435e-03 0.9460726478
## 141 -0.65719989 13.86171 2.434695e-01 0.6217274277
## 142 -3.94949512 13.59318 7.263389e+00 0.0070547910
## 143 0.54143801 13.50619 1.784281e-01 0.6727410196
## 144 -0.37406772 13.51319 8.835793e-02 0.7662842898
## 145 -3.52769161 13.64231 5.830998e+00 0.0157724846
## 146 -2.82522997 13.58344 3.914429e+00 0.0479136767
## 147 -2.71355433 13.80321 3.464247e+00 0.0627522949
## 148 -2.40752868 13.65672 3.190782e+00 0.0740992453
## 149 -0.52654232 13.82271 1.803118e-01 0.6711188628
## 150 -2.66984684 13.69927 3.476830e+00 0.0622770158
## 151 -3.51757414 13.52578 6.021980e+00 0.0141537612
## 152 -0.82345512 13.61441 3.999886e-01 0.5271164906
## 153 -0.56923983 13.67875 1.775067e-01 0.6735380998
## 154 3.40505697 13.52226 5.695708e+00 0.0170337107
## 155 0.00000000 13.50153 0.000000e+00 1.0000000000
## 156 -2.44172064 13.48247 3.406623e+00 0.0649787736
## 157 1.61864051 13.41433 1.544650e+00 0.2139699987
## 158 3.12035816 13.66797 4.833711e+00 0.0279421539
## 159 -2.38990623 13.54292 2.869234e+00 0.0903337814
## 160 -0.07031125 13.41277 3.398600e-03 0.9535133684
## 161 -1.24983497 13.64195 8.901423e-01 0.3454723568
## 162 -1.56940752 13.77526 1.255549e+00 0.2625349407
## 163 -4.06143494 13.88829 7.485774e+00 0.0062350224
## 164 -1.33698648 13.86218 1.349144e+00 0.2454687124
## 165 -1.33662302 13.70645 1.318547e+00 0.2508934441
## 166 -1.45342750 13.84808 1.286846e+00 0.2566701216
## 167 -1.15138805 13.56118 7.844221e-01 0.3758235301
## 168 1.36865121 13.71953 1.324760e+00 0.2497801323
## 169 -1.69837784 13.51527 1.493630e+00 0.2216965949
## 170 -1.53955965 13.65593 1.208879e+00 0.2715932279
## 171 -0.31574511 13.88660 6.508969e-02 0.7986328926
## 172 -0.42048423 13.51247 1.020384e-01 0.7494069115
## 173 0.00000000 13.70794 0.000000e+00 1.0000000000
## 174 0.04392314 13.55632 2.499763e-03 0.9601257463
## 175 -1.07826692 13.59432 6.380833e-01 0.4244336910
## 176 -3.13185706 13.56699 4.862113e+00 0.0274861413
## 177 2.27767180 13.57786 2.939585e+00 0.0864786471
## 178 0.00000000 13.80222 0.000000e+00 1.0000000000
## 179 3.74153522 13.62608 6.567182e+00 0.0104090271
## 180 -1.25358047 13.94693 1.256116e+00 0.2624272465
## 181 -3.94954323 13.58928 7.275358e+00 0.0070079844
## 182 -1.52750117 13.42415 1.281721e+00 0.2576192772
## 183 4.53082669 13.45381 9.523683e+00 0.0020365491
## 184 0.00000000 13.64417 0.000000e+00 1.0000000000
## 185 -4.63677049 13.53305 9.507793e+00 0.0020542347
## 186 -1.33676194 13.75370 1.333524e+00 0.2482200018
## 187 0.45869398 13.56051 1.329725e-01 0.7153811214
## 188 -1.31571639 13.56373 1.401112e+00 0.2365789880
## 189 -2.90410496 13.57654 4.360645e+00 0.0368155949
## 190 -1.27732629 13.54894 9.087419e-01 0.3404824352
## 191 -0.91835231 13.47739 5.039700e-01 0.4777853297
## 192 0.00000000 13.80537 0.000000e+00 1.0000000000
## 193 -0.37464165 13.66993 8.847414e-02 0.7661351139
## 194 -2.77266134 13.48646 4.148335e+00 0.0417142652
## 195 0.00000000 13.83672 0.000000e+00 1.0000000000
## 196 2.30381078 13.52103 2.872497e+00 0.0901508753
## 197 -0.55783698 13.57134 1.653240e-01 0.6843141916
## 198 -2.76088809 13.51103 4.095544e+00 0.0430355432
## 199 1.03525315 13.60980 6.568446e-01 0.4177045651
## 200 -1.30842799 13.57503 9.225281e-01 0.3368463019
## 201 -1.65184282 13.50101 1.424634e+00 0.2326839120
## 202 -1.88158957 13.82907 2.245531e+00 0.1340474886
## 203 -0.36833045 13.72669 8.221213e-02 0.7743304441
## 204 0.62880398 13.58713 2.528018e-01 0.6151254554
## 205 1.69009583 13.58386 1.681897e+00 0.1947166979
## 206 0.67745905 13.81410 3.002774e-01 0.5837266354
## 207 3.43196492 13.52587 5.733955e+00 0.0166669568
## 208 -1.86358405 13.62816 1.730402e+00 0.1884040710
## 209 -1.86398470 13.66434 1.796548e+00 0.1801752549
## 210 1.21974017 13.54584 8.889966e-01 0.3457829468
## 211 -0.28938405 13.71904 4.820422e-02 0.8262246725
## 212 -0.42723803 13.57691 1.149933e-01 0.7345399522
## 213 0.80517251 13.46214 3.868702e-01 0.5339701013
## 214 -1.09000453 13.90578 7.741478e-01 0.3789681180
## 215 -0.91669965 13.64604 5.005496e-01 0.4792830385
## 216 0.00000000 13.49761 0.000000e+00 1.0000000000
## 217 -1.22950239 13.76248 8.677402e-01 0.3516148359
## 218 0.21528167 13.41378 3.136478e-02 0.8594343031
## 219 -0.35634244 13.52859 7.229845e-02 0.7880273589
## 220 0.04851715 13.57385 1.829581e-03 0.9658832647
## 221 0.00000000 13.42775 0.000000e+00 1.0000000000
## 222 -3.10072377 13.61755 4.809924e+00 0.0283301405
## 223 -3.01964678 13.56730 4.526150e+00 0.0334166247
## 224 -0.61908142 13.48547 2.108293e-01 0.6461328707
## 225 -0.42938460 13.87815 1.221514e-01 0.7267236316
## 226 0.00000000 13.40892 0.000000e+00 1.0000000000
## 227 -1.24837564 13.45634 1.374628e+00 0.2410594331
## 228 1.36727897 13.85833 1.351456e+00 0.2450647290
## 229 0.00000000 13.78537 0.000000e+00 1.0000000000
## 230 0.11215585 13.43765 6.277143e-03 0.9368532769
## 231 0.00000000 13.66657 0.000000e+00 1.0000000000
## 232 -1.31627095 13.75876 1.317710e+00 0.2510439135
## 233 -0.94889390 13.43024 5.091920e-01 0.4755134190
## 234 -1.63980828 13.46556 1.428453e+00 0.2320589393
## 235 -2.06859665 13.61061 2.066790e+00 0.1505841821
## 236 -2.05297191 13.39390 2.359702e+00 0.1245526383
## 237 -2.26582310 13.39949 2.983026e+00 0.0841873686
## 238 -1.31566623 13.58556 1.394975e+00 0.2376082047
## 239 0.00000000 13.69667 0.000000e+00 1.0000000000
## 240 2.20220727 13.56852 2.777159e+00 0.0956638465
## 241 -1.98075636 13.54303 2.492872e+00 0.1144094955
## 242 -1.32979840 13.46732 9.546773e-01 0.3285664397
## 243 -0.83548140 13.51974 4.185770e-01 0.5176698605
## 244 -3.21703776 13.69463 4.744376e+00 0.0294285612
## 245 0.26073661 13.68221 4.257120e-02 0.8365409769
## 246 0.00000000 13.46182 0.000000e+00 1.0000000000
## 247 -4.26410628 13.79930 7.911559e+00 0.0049261206
## 248 -1.94547626 13.55522 2.443783e+00 0.1180380137
## 249 0.00000000 13.77484 0.000000e+00 1.0000000000
## 250 0.00000000 13.69342 0.000000e+00 1.0000000000
## 251 -2.44165423 13.69297 3.167820e+00 0.0751473886
## 252 4.91547331 13.54614 1.054609e+01 0.0011700077
## 253 -2.47814678 13.58956 3.440127e+00 0.0636741684
## 254 -0.29480525 13.44809 4.311958e-02 0.8355065060
## 255 0.00000000 13.45952 0.000000e+00 1.0000000000
## 256 -2.20812283 13.58750 2.739230e+00 0.0979582282
## 257 -3.80536109 13.86087 6.725588e+00 0.0095243673
## 258 -5.07638464 13.79962 1.062144e+01 0.0011233514
## 259 0.00000000 13.67408 0.000000e+00 1.0000000000
## 260 0.29068958 13.58925 5.192085e-02 0.8197608104
## 261 -2.10012989 13.66979 2.186642e+00 0.1392590271
## 262 0.00000000 13.74541 0.000000e+00 1.0000000000
## 263 -1.63946007 13.89494 1.442257e+00 0.2298164248
## 264 -0.22152673 13.54468 2.960862e-02 0.8633864054
## 265 -0.44400099 13.49555 1.098303e-01 0.7403476123
## 266 -3.04233111 13.66067 4.566750e+00 0.0326340282
## 267 1.29247040 13.79312 8.708102e-01 0.3507643511
## 268 -1.33650441 13.65793 1.357424e+00 0.2440254337
## 269 -0.38261307 13.66642 7.961416e-02 0.7778295775
## 270 -4.16536238 13.47636 8.037301e+00 0.0045959361
## 271 0.00000000 13.85562 0.000000e+00 1.0000000000
## 272 -1.08680272 13.54191 6.293198e-01 0.4276326756
## 273 -1.98050063 13.41423 2.640581e+00 0.1042118914
## 274 1.20220549 13.56375 9.180922e-01 0.3380105552
## 275 3.08727262 13.75638 4.662158e+00 0.0308693830
## 276 -1.86908815 13.60569 1.957429e+00 0.1618342645
## 277 -2.43229100 13.76114 3.193650e+00 0.0739694540
## 278 -2.66067396 13.53443 3.717613e+00 0.0538829923
## 279 2.57782107 13.54565 3.597599e+00 0.0579055339
## 280 -2.91995836 13.60660 4.475521e+00 0.0344200749
## 281 -3.43359249 13.65082 5.476684e+00 0.0193006307
## 282 0.59981879 13.52173 2.129113e-01 0.6445098979
## 283 -1.33659833 13.69892 1.319646e+00 0.2506961732
## 284 -1.68095504 13.51466 1.466492e+00 0.2259422773
## 285 -3.21644667 13.52154 5.098893e+00 0.0239727751
## 286 0.26322545 13.84464 6.345723e-02 0.8011204477
## 287 -0.53787263 13.52760 1.816098e-01 0.6700069553
## 288 2.11590794 13.66685 2.710272e+00 0.0997503480
## 289 0.00000000 13.99319 0.000000e+00 1.0000000000
## 290 -3.70223008 13.48070 6.537382e+00 0.0105846538
## 291 -1.66080445 13.45793 1.693337e+00 0.2351135572
## 292 -0.91775849 13.47710 4.685829e-01 0.4936632176
## 293 -1.16353159 13.69881 7.195659e-01 0.3963162771
## 294 -1.48886730 13.41388 1.307153e+00 0.2529510897
## 295 -2.96470911 13.54063 4.480592e+00 0.0343181782
## 296 1.25972948 13.40038 1.020622e+00 0.3124076273
## 297 -2.12188549 13.69891 2.103506e+00 0.1470080448
## 298 -0.79677606 13.39035 3.505820e-01 0.5538036049
## 299 -1.24773542 13.64418 1.297645e+00 0.2546841046
## 300 -1.98010596 13.66039 2.371539e+00 0.1236118419
## 301 0.19144852 13.69050 2.261618e-02 0.8804639441
## 302 -1.24830749 13.60613 1.328617e+00 0.2490920566
## 303 0.27093470 13.50957 4.569560e-02 0.8455992580
## 304 -1.07384031 13.56723 5.068467e-01 0.5466069342
## 305 3.11675308 13.58036 4.737588e+00 0.0295448126
## 306 0.50426850 13.43894 1.614357e-01 0.6878508129
## 307 -3.45029759 13.85775 5.468350e+00 0.0193928114
## 308 -1.16017641 13.66652 7.592196e-01 0.3836036999
## 309 -2.55004334 13.75221 3.149722e+00 0.0759847473
## 310 0.13424667 13.58796 1.002867e-02 0.9202335611
## 311 -3.79270158 13.39403 7.405370e+00 0.0065195498
## 312 5.17376692 13.63839 1.090563e+01 0.0009636872
## 313 2.08788166 13.53486 2.494012e+00 0.1143267122
## 314 -1.05980083 13.59877 6.087661e-01 0.4352799991
## 315 0.00000000 13.70726 0.000000e+00 1.0000000000
## 316 -1.95865407 13.83024 2.339465e+00 0.1261795445
## 317 0.00000000 13.52662 0.000000e+00 1.0000000000
## 318 0.16558678 13.77083 1.778865e-02 0.8939014967
## 319 -1.87605343 13.47984 2.358904e+00 0.1246163310
## 320 -2.99579054 13.54417 4.429824e+00 0.0353528584
## 321 -3.61169447 13.56815 6.336298e+00 0.0118520219
## 322 -1.08244734 13.67284 5.853721e-01 0.4442409190
## 323 -0.30604063 13.71216 5.276730e-02 0.8183230056
## 324 -3.00272346 13.56970 4.546381e+00 0.0330242342
## 325 -1.53203979 13.65326 1.178992e+00 0.2775998424
## 326 -1.36066455 13.53968 1.058969e+00 0.3034871072
## 327 -0.01543818 13.62384 9.329385e-04 0.9756340680
## 328 -1.83011136 13.67637 1.644412e+00 0.1997650948
## 329 -0.68944662 13.45508 2.811690e-01 0.5959533903
## 330 -0.37171909 13.72996 8.156986e-02 0.7751898734
## 331 -1.19113831 13.67317 7.744748e-01 0.3788674778
## 332 -2.47809854 13.47457 3.476174e+00 0.0623017278
## 333 3.09751207 13.49352 4.787386e+00 0.0287029257
## 334 -1.24802971 13.62387 1.311693e+00 0.2521288237
## 335 1.57809424 13.49597 1.358698e+00 0.2438043275
## 336 -1.26845475 13.50243 9.251873e-01 0.3361509255
## 337 2.44475662 13.59264 3.171226e+00 0.0749909326
## 338 -1.80624811 13.56742 1.829912e+00 0.1761831000
## 339 -0.44342172 13.53989 1.224292e-01 0.7264254592
## FDR Nhood SpatialFDR contrast
## 1 1.0000000 1 1.0000000 Age1wk - Age4wk
## 2 0.5016543 2 0.5174654 Age1wk - Age4wk
## 3 1.0000000 3 1.0000000 Age1wk - Age4wk
## 4 0.8515624 4 0.8711589 Age1wk - Age4wk
## 5 0.2047089 5 0.2108180 Age1wk - Age4wk
## 6 0.5069113 6 0.5246127 Age1wk - Age4wk
## 7 0.7164668 7 0.7390460 Age1wk - Age4wk
## 8 0.2047089 8 0.2108180 Age1wk - Age4wk
## 9 1.0000000 9 1.0000000 Age1wk - Age4wk
## 10 0.1294448 10 0.1296490 Age1wk - Age4wk
## 11 0.9513726 11 0.9651099 Age1wk - Age4wk
## 12 0.5390922 12 0.5488093 Age1wk - Age4wk
## 13 0.9301601 13 0.9512893 Age1wk - Age4wk
## 14 0.8161409 14 0.8340011 Age1wk - Age4wk
## 15 1.0000000 15 1.0000000 Age1wk - Age4wk
## 16 1.0000000 16 1.0000000 Age1wk - Age4wk
## 17 1.0000000 17 1.0000000 Age1wk - Age4wk
## 18 0.4322204 18 0.4461411 Age1wk - Age4wk
## 19 0.6547381 19 0.6625748 Age1wk - Age4wk
## 20 0.5277872 20 0.5488093 Age1wk - Age4wk
## 21 0.1395437 21 0.1515522 Age1wk - Age4wk
## 22 0.4221712 22 0.4350017 Age1wk - Age4wk
## 23 0.9405711 23 0.9570125 Age1wk - Age4wk
## 24 0.3384004 24 0.3490185 Age1wk - Age4wk
## 25 0.1395437 25 0.1515522 Age1wk - Age4wk
## 26 0.8834077 26 0.9036704 Age1wk - Age4wk
## 27 0.8515624 27 0.8711589 Age1wk - Age4wk
## 28 0.4564257 28 0.4755424 Age1wk - Age4wk
## 29 0.5390922 29 0.5488093 Age1wk - Age4wk
## 30 0.7164668 30 0.7390460 Age1wk - Age4wk
## 31 1.0000000 31 1.0000000 Age1wk - Age4wk
## 32 0.3704967 32 0.3781165 Age1wk - Age4wk
## 33 0.8834077 33 0.9034535 Age1wk - Age4wk
## 34 0.7164668 34 0.7390460 Age1wk - Age4wk
## 35 0.5390922 35 0.5488093 Age1wk - Age4wk
## 36 0.1328652 36 0.1365070 Age1wk - Age4wk
## 37 0.8281076 37 0.8451428 Age1wk - Age4wk
## 38 0.7527405 38 0.7705335 Age1wk - Age4wk
## 39 1.0000000 39 1.0000000 Age1wk - Age4wk
## 40 0.6604069 40 0.6728621 Age1wk - Age4wk
## 41 0.5086131 41 0.5279530 Age1wk - Age4wk
## 42 0.8277834 42 0.8451428 Age1wk - Age4wk
## 43 1.0000000 43 1.0000000 Age1wk - Age4wk
## 44 0.1395437 44 0.1515522 Age1wk - Age4wk
## 45 0.2031693 45 0.2108180 Age1wk - Age4wk
## 46 1.0000000 46 1.0000000 Age1wk - Age4wk
## 47 0.5390922 47 0.5488093 Age1wk - Age4wk
## 48 1.0000000 48 1.0000000 Age1wk - Age4wk
## 49 1.0000000 49 1.0000000 Age1wk - Age4wk
## 50 0.1226114 50 0.1296490 Age1wk - Age4wk
## 51 0.5390922 51 0.5488093 Age1wk - Age4wk
## 52 0.2047089 52 0.2108180 Age1wk - Age4wk
## 53 0.8630330 53 0.8772666 Age1wk - Age4wk
## 54 0.9812909 54 0.9831615 Age1wk - Age4wk
## 55 0.5390922 55 0.5488093 Age1wk - Age4wk
## 56 1.0000000 56 0.9949737 Age1wk - Age4wk
## 57 0.9513726 57 0.9651099 Age1wk - Age4wk
## 58 1.0000000 58 1.0000000 Age1wk - Age4wk
## 59 0.7164668 59 0.7390460 Age1wk - Age4wk
## 60 1.0000000 60 1.0000000 Age1wk - Age4wk
## 61 1.0000000 61 1.0000000 Age1wk - Age4wk
## 62 0.5390922 62 0.5488093 Age1wk - Age4wk
## 63 0.1395437 63 0.1515522 Age1wk - Age4wk
## 64 1.0000000 64 1.0000000 Age1wk - Age4wk
## 65 1.0000000 65 1.0000000 Age1wk - Age4wk
## 66 0.1294448 66 0.1296490 Age1wk - Age4wk
## 67 0.6833521 67 0.6958646 Age1wk - Age4wk
## 68 0.5965844 68 0.6052819 Age1wk - Age4wk
## 69 0.2976040 69 0.2946432 Age1wk - Age4wk
## 70 1.0000000 70 1.0000000 Age1wk - Age4wk
## 71 0.4680500 71 0.4875123 Age1wk - Age4wk
## 72 1.0000000 72 1.0000000 Age1wk - Age4wk
## 73 0.7669508 73 0.7856152 Age1wk - Age4wk
## 74 1.0000000 74 1.0000000 Age1wk - Age4wk
## 75 1.0000000 75 1.0000000 Age1wk - Age4wk
## 76 0.8748848 76 0.8907601 Age1wk - Age4wk
## 77 0.1966838 77 0.2108180 Age1wk - Age4wk
## 78 0.2047089 78 0.2108180 Age1wk - Age4wk
## 79 0.3219854 79 0.3303003 Age1wk - Age4wk
## 80 0.5390922 80 0.5488093 Age1wk - Age4wk
## 81 0.5069113 81 0.5246127 Age1wk - Age4wk
## 82 1.0000000 82 1.0000000 Age1wk - Age4wk
## 83 1.0000000 83 1.0000000 Age1wk - Age4wk
## 84 1.0000000 84 1.0000000 Age1wk - Age4wk
## 85 1.0000000 85 1.0000000 Age1wk - Age4wk
## 86 1.0000000 86 1.0000000 Age1wk - Age4wk
## 87 0.4193614 87 0.4295266 Age1wk - Age4wk
## 88 0.9513726 88 0.9651099 Age1wk - Age4wk
## 89 0.6547381 89 0.6625748 Age1wk - Age4wk
## 90 0.1388160 90 0.1440254 Age1wk - Age4wk
## 91 0.5390922 91 0.5488093 Age1wk - Age4wk
## 92 0.1012522 92 0.1035243 Age1wk - Age4wk
## 93 0.4193614 93 0.4295266 Age1wk - Age4wk
## 94 0.2047089 94 0.2108180 Age1wk - Age4wk
## 95 0.9933137 95 0.9927464 Age1wk - Age4wk
## 96 0.4221712 96 0.4324996 Age1wk - Age4wk
## 97 0.1963319 97 0.2108180 Age1wk - Age4wk
## 98 0.4564257 98 0.4755424 Age1wk - Age4wk
## 99 0.5862198 99 0.5986355 Age1wk - Age4wk
## 100 0.3704967 100 0.3781165 Age1wk - Age4wk
## 101 1.0000000 101 1.0000000 Age1wk - Age4wk
## 102 1.0000000 102 1.0000000 Age1wk - Age4wk
## 103 0.5151161 103 0.5378106 Age1wk - Age4wk
## 104 0.6833521 104 0.6958646 Age1wk - Age4wk
## 105 0.3562892 105 0.3621768 Age1wk - Age4wk
## 106 0.9933137 106 0.9927464 Age1wk - Age4wk
## 107 1.0000000 107 1.0000000 Age1wk - Age4wk
## 108 0.1660377 108 0.1757241 Age1wk - Age4wk
## 109 0.2011609 109 0.2108180 Age1wk - Age4wk
## 110 1.0000000 110 1.0000000 Age1wk - Age4wk
## 111 0.3039004 111 0.3010781 Age1wk - Age4wk
## 112 0.9513726 112 0.9651099 Age1wk - Age4wk
## 113 0.9934689 113 0.9927464 Age1wk - Age4wk
## 114 0.5086131 114 0.5300257 Age1wk - Age4wk
## 115 0.8178190 115 0.8364714 Age1wk - Age4wk
## 116 0.3219854 116 0.3303003 Age1wk - Age4wk
## 117 1.0000000 117 1.0000000 Age1wk - Age4wk
## 118 0.9191510 118 0.9399306 Age1wk - Age4wk
## 119 1.0000000 119 1.0000000 Age1wk - Age4wk
## 120 0.3039004 120 0.3010781 Age1wk - Age4wk
## 121 0.7162299 121 0.7343263 Age1wk - Age4wk
## 122 0.7067490 122 0.7246676 Age1wk - Age4wk
## 123 0.5390922 123 0.5488093 Age1wk - Age4wk
## 124 1.0000000 124 1.0000000 Age1wk - Age4wk
## 125 0.1294448 125 0.1296490 Age1wk - Age4wk
## 126 0.4193614 126 0.4295266 Age1wk - Age4wk
## 127 0.3219854 127 0.3227886 Age1wk - Age4wk
## 128 0.1012522 128 0.1035243 Age1wk - Age4wk
## 129 0.2011609 129 0.2108180 Age1wk - Age4wk
## 130 0.5390922 130 0.5488093 Age1wk - Age4wk
## 131 0.9933137 131 0.9927464 Age1wk - Age4wk
## 132 1.0000000 132 1.0000000 Age1wk - Age4wk
## 133 1.0000000 133 1.0000000 Age1wk - Age4wk
## 134 1.0000000 134 1.0000000 Age1wk - Age4wk
## 135 1.0000000 135 1.0000000 Age1wk - Age4wk
## 136 0.7494038 136 0.7662373 Age1wk - Age4wk
## 137 0.5862198 137 0.5986355 Age1wk - Age4wk
## 138 0.4221712 138 0.4350017 Age1wk - Age4wk
## 139 1.0000000 139 1.0000000 Age1wk - Age4wk
## 140 1.0000000 140 1.0000000 Age1wk - Age4wk
## 141 0.9244105 141 0.9452524 Age1wk - Age4wk
## 142 0.1328652 142 0.1365070 Age1wk - Age4wk
## 143 0.9513726 143 0.9651099 Age1wk - Age4wk
## 144 1.0000000 144 1.0000000 Age1wk - Age4wk
## 145 0.1782291 145 0.1901915 Age1wk - Age4wk
## 146 0.2619796 146 0.2594111 Age1wk - Age4wk
## 147 0.3039004 147 0.3010781 Age1wk - Age4wk
## 148 0.3219854 148 0.3303003 Age1wk - Age4wk
## 149 0.9513726 149 0.9651099 Age1wk - Age4wk
## 150 0.3039004 150 0.3010781 Age1wk - Age4wk
## 151 0.1660377 151 0.1757241 Age1wk - Age4wk
## 152 0.8350116 152 0.8532802 Age1wk - Age4wk
## 153 0.9513726 153 0.9651099 Age1wk - Age4wk
## 154 0.1804509 154 0.1911862 Age1wk - Age4wk
## 155 1.0000000 155 1.0000000 Age1wk - Age4wk
## 156 0.3059417 156 0.3015523 Age1wk - Age4wk
## 157 0.5390922 157 0.5488093 Age1wk - Age4wk
## 158 0.2047089 158 0.2108180 Age1wk - Age4wk
## 159 0.3562892 159 0.3621768 Age1wk - Age4wk
## 160 1.0000000 160 1.0000000 Age1wk - Age4wk
## 161 0.6547381 161 0.6625748 Age1wk - Age4wk
## 162 0.5426789 162 0.5543823 Age1wk - Age4wk
## 163 0.1328652 163 0.1365070 Age1wk - Age4wk
## 164 0.5390922 164 0.5488093 Age1wk - Age4wk
## 165 0.5390922 165 0.5488093 Age1wk - Age4wk
## 166 0.5390922 166 0.5488093 Age1wk - Age4wk
## 167 0.6833521 167 0.6958646 Age1wk - Age4wk
## 168 0.5390922 168 0.5488093 Age1wk - Age4wk
## 169 0.5390922 169 0.5488093 Age1wk - Age4wk
## 170 0.5580006 170 0.5712136 Age1wk - Age4wk
## 171 1.0000000 171 1.0000000 Age1wk - Age4wk
## 172 1.0000000 172 0.9949737 Age1wk - Age4wk
## 173 1.0000000 173 1.0000000 Age1wk - Age4wk
## 174 1.0000000 174 1.0000000 Age1wk - Age4wk
## 175 0.7266819 175 0.7486393 Age1wk - Age4wk
## 176 0.2047089 176 0.2108180 Age1wk - Age4wk
## 177 0.3532080 177 0.3608202 Age1wk - Age4wk
## 178 1.0000000 178 1.0000000 Age1wk - Age4wk
## 179 0.1395437 179 0.1515522 Age1wk - Age4wk
## 180 0.5426789 180 0.5543823 Age1wk - Age4wk
## 181 0.1328652 181 0.1365070 Age1wk - Age4wk
## 182 0.5390922 182 0.5488093 Age1wk - Age4wk
## 183 0.1012522 183 0.1035243 Age1wk - Age4wk
## 184 1.0000000 184 1.0000000 Age1wk - Age4wk
## 185 0.1012522 185 0.1035243 Age1wk - Age4wk
## 186 0.5390922 186 0.5488093 Age1wk - Age4wk
## 187 0.9933137 187 0.9927464 Age1wk - Age4wk
## 188 0.5390922 188 0.5488093 Age1wk - Age4wk
## 189 0.2115337 189 0.2173355 Age1wk - Age4wk
## 190 0.6547381 190 0.6611470 Age1wk - Age4wk
## 191 0.7849128 191 0.8041576 Age1wk - Age4wk
## 192 1.0000000 192 1.0000000 Age1wk - Age4wk
## 193 1.0000000 193 1.0000000 Age1wk - Age4wk
## 194 0.2356856 194 0.2363220 Age1wk - Age4wk
## 195 1.0000000 195 1.0000000 Age1wk - Age4wk
## 196 0.3562892 196 0.3621768 Age1wk - Age4wk
## 197 0.9625830 197 0.9685744 Age1wk - Age4wk
## 198 0.2391647 198 0.2382813 Age1wk - Age4wk
## 199 0.7187911 199 0.7418921 Age1wk - Age4wk
## 200 0.6547381 200 0.6595244 Age1wk - Age4wk
## 201 0.5390922 201 0.5488093 Age1wk - Age4wk
## 202 0.4286990 202 0.4427614 Age1wk - Age4wk
## 203 1.0000000 203 1.0000000 Age1wk - Age4wk
## 204 0.9191510 204 0.9399306 Age1wk - Age4wk
## 205 0.5280717 205 0.5488093 Age1wk - Age4wk
## 206 0.8834077 206 0.9036704 Age1wk - Age4wk
## 207 0.1804509 207 0.1911862 Age1wk - Age4wk
## 208 0.5192600 208 0.5403206 Age1wk - Age4wk
## 209 0.5086131 209 0.5287291 Age1wk - Age4wk
## 210 0.6547381 210 0.6625748 Age1wk - Age4wk
## 211 1.0000000 211 1.0000000 Age1wk - Age4wk
## 212 0.9934689 212 0.9927464 Age1wk - Age4wk
## 213 0.8419343 213 0.8591986 Age1wk - Age4wk
## 214 0.6833521 214 0.6958646 Age1wk - Age4wk
## 215 0.7849128 215 0.8041576 Age1wk - Age4wk
## 216 1.0000000 216 1.0000000 Age1wk - Age4wk
## 217 0.6549309 217 0.6662429 Age1wk - Age4wk
## 218 1.0000000 218 1.0000000 Age1wk - Age4wk
## 219 1.0000000 219 1.0000000 Age1wk - Age4wk
## 220 1.0000000 220 1.0000000 Age1wk - Age4wk
## 221 1.0000000 221 1.0000000 Age1wk - Age4wk
## 222 0.2047089 222 0.2108180 Age1wk - Age4wk
## 223 0.2047089 223 0.2108180 Age1wk - Age4wk
## 224 0.9441338 224 0.9600572 Age1wk - Age4wk
## 225 0.9933137 225 0.9927464 Age1wk - Age4wk
## 226 1.0000000 226 1.0000000 Age1wk - Age4wk
## 227 0.5390922 227 0.5488093 Age1wk - Age4wk
## 228 0.5390922 228 0.5488093 Age1wk - Age4wk
## 229 1.0000000 229 1.0000000 Age1wk - Age4wk
## 230 1.0000000 230 1.0000000 Age1wk - Age4wk
## 231 1.0000000 231 1.0000000 Age1wk - Age4wk
## 232 0.5390922 232 0.5488093 Age1wk - Age4wk
## 233 0.7849128 233 0.8041576 Age1wk - Age4wk
## 234 0.5390922 234 0.5488093 Age1wk - Age4wk
## 235 0.4564257 235 0.4755424 Age1wk - Age4wk
## 236 0.4193614 236 0.4295266 Age1wk - Age4wk
## 237 0.3480429 237 0.3537779 Age1wk - Age4wk
## 238 0.5390922 238 0.5488093 Age1wk - Age4wk
## 239 1.0000000 239 1.0000000 Age1wk - Age4wk
## 240 0.3704967 240 0.3779342 Age1wk - Age4wk
## 241 0.4126045 241 0.4230634 Age1wk - Age4wk
## 242 0.6475815 242 0.6531982 Age1wk - Age4wk
## 243 0.8277834 243 0.8451428 Age1wk - Age4wk
## 244 0.2047089 244 0.2108180 Age1wk - Age4wk
## 245 1.0000000 245 1.0000000 Age1wk - Age4wk
## 246 1.0000000 246 1.0000000 Age1wk - Age4wk
## 247 0.1294448 247 0.1296490 Age1wk - Age4wk
## 248 0.4193614 248 0.4295266 Age1wk - Age4wk
## 249 1.0000000 249 1.0000000 Age1wk - Age4wk
## 250 1.0000000 250 1.0000000 Age1wk - Age4wk
## 251 0.3219854 251 0.3303003 Age1wk - Age4wk
## 252 0.1012522 252 0.1035243 Age1wk - Age4wk
## 253 0.3040217 253 0.3010781 Age1wk - Age4wk
## 254 1.0000000 254 1.0000000 Age1wk - Age4wk
## 255 1.0000000 255 1.0000000 Age1wk - Age4wk
## 256 0.3704967 256 0.3781165 Age1wk - Age4wk
## 257 0.1395437 257 0.1515522 Age1wk - Age4wk
## 258 0.1012522 258 0.1035243 Age1wk - Age4wk
## 259 1.0000000 259 1.0000000 Age1wk - Age4wk
## 260 1.0000000 260 1.0000000 Age1wk - Age4wk
## 261 0.4371186 261 0.4523858 Age1wk - Age4wk
## 262 1.0000000 262 1.0000000 Age1wk - Age4wk
## 263 0.5390922 263 0.5488093 Age1wk - Age4wk
## 264 1.0000000 264 1.0000000 Age1wk - Age4wk
## 265 0.9959438 265 0.9949737 Age1wk - Age4wk
## 266 0.2047089 266 0.2108180 Age1wk - Age4wk
## 267 0.6549309 267 0.6662429 Age1wk - Age4wk
## 268 0.5390922 268 0.5488093 Age1wk - Age4wk
## 269 1.0000000 269 1.0000000 Age1wk - Age4wk
## 270 0.1294448 270 0.1296490 Age1wk - Age4wk
## 271 1.0000000 271 1.0000000 Age1wk - Age4wk
## 272 0.7284798 272 0.7486393 Age1wk - Age4wk
## 273 0.3839982 273 0.3939420 Age1wk - Age4wk
## 274 0.6547381 274 0.6595244 Age1wk - Age4wk
## 275 0.2047089 275 0.2108180 Age1wk - Age4wk
## 276 0.4812440 276 0.5001279 Age1wk - Age4wk
## 277 0.3219854 277 0.3303003 Age1wk - Age4wk
## 278 0.2899418 278 0.2874111 Age1wk - Age4wk
## 279 0.3019996 279 0.3007969 Age1wk - Age4wk
## 280 0.2047089 280 0.2108180 Age1wk - Age4wk
## 281 0.1933577 281 0.2092038 Age1wk - Age4wk
## 282 0.9441338 282 0.9600572 Age1wk - Age4wk
## 283 0.5390922 283 0.5488093 Age1wk - Age4wk
## 284 0.5390922 284 0.5488093 Age1wk - Age4wk
## 285 0.2031693 285 0.2108180 Age1wk - Age4wk
## 286 1.0000000 286 1.0000000 Age1wk - Age4wk
## 287 0.9513726 287 0.9651099 Age1wk - Age4wk
## 288 0.3715975 288 0.3815324 Age1wk - Age4wk
## 289 1.0000000 289 1.0000000 Age1wk - Age4wk
## 290 0.1395437 290 0.1515522 Age1wk - Age4wk
## 291 0.5390922 291 0.5488093 Age1wk - Age4wk
## 292 0.8045761 292 0.8229023 Age1wk - Age4wk
## 293 0.7067490 293 0.7228042 Age1wk - Age4wk
## 294 0.5390922 294 0.5488093 Age1wk - Age4wk
## 295 0.2047089 295 0.2108180 Age1wk - Age4wk
## 296 0.6193344 296 0.6251441 Age1wk - Age4wk
## 297 0.4564257 297 0.4745536 Age1wk - Age4wk
## 298 0.8572576 298 0.8711589 Age1wk - Age4wk
## 299 0.5390922 299 0.5488093 Age1wk - Age4wk
## 300 0.4193614 300 0.4295266 Age1wk - Age4wk
## 301 1.0000000 301 1.0000000 Age1wk - Age4wk
## 302 0.5390922 302 0.5488093 Age1wk - Age4wk
## 303 1.0000000 303 1.0000000 Age1wk - Age4wk
## 304 0.8515624 304 0.8711589 Age1wk - Age4wk
## 305 0.2047089 305 0.2108180 Age1wk - Age4wk
## 306 0.9635596 306 0.9685744 Age1wk - Age4wk
## 307 0.1933577 307 0.2092038 Age1wk - Age4wk
## 308 0.6880511 308 0.7019225 Age1wk - Age4wk
## 309 0.3219854 309 0.3315943 Age1wk - Age4wk
## 310 1.0000000 310 1.0000000 Age1wk - Age4wk
## 311 0.1328652 311 0.1365070 Age1wk - Age4wk
## 312 0.1012522 312 0.1035243 Age1wk - Age4wk
## 313 0.4126045 313 0.4230634 Age1wk - Age4wk
## 314 0.7377996 314 0.7593725 Age1wk - Age4wk
## 315 1.0000000 315 1.0000000 Age1wk - Age4wk
## 316 0.4193614 316 0.4295266 Age1wk - Age4wk
## 317 1.0000000 317 1.0000000 Age1wk - Age4wk
## 318 1.0000000 318 1.0000000 Age1wk - Age4wk
## 319 0.4193614 319 0.4295266 Age1wk - Age4wk
## 320 0.2066314 320 0.2126535 Age1wk - Age4wk
## 321 0.1488087 321 0.1622165 Age1wk - Age4wk
## 322 0.7492421 322 0.7662373 Age1wk - Age4wk
## 323 1.0000000 323 1.0000000 Age1wk - Age4wk
## 324 0.2047089 324 0.2108180 Age1wk - Age4wk
## 325 0.5669057 325 0.5787362 Age1wk - Age4wk
## 326 0.6051890 326 0.6106283 Age1wk - Age4wk
## 327 1.0000000 327 1.0000000 Age1wk - Age4wk
## 328 0.5374632 328 0.5488093 Age1wk - Age4wk
## 329 0.8979031 329 0.9151157 Age1wk - Age4wk
## 330 1.0000000 330 1.0000000 Age1wk - Age4wk
## 331 0.6833521 331 0.6958646 Age1wk - Age4wk
## 332 0.3039004 332 0.3010781 Age1wk - Age4wk
## 333 0.2047089 333 0.2108180 Age1wk - Age4wk
## 334 0.5390922 334 0.5488093 Age1wk - Age4wk
## 335 0.5390922 335 0.5488093 Age1wk - Age4wk
## 336 0.6547381 336 0.6595244 Age1wk - Age4wk
## 337 0.3219854 337 0.3303003 Age1wk - Age4wk
## 338 0.5069113 338 0.5246127 Age1wk - Age4wk
## 339 0.9933137 339 0.9927464 Age1wk - Age4wk
## PValue_adj_withinNhood
## 1 0.8029741404
## 2 0.1701777150
## 3 0.9126920869
## 4 0.5466069277
## 5 0.0261032547
## 6 0.1763459652
## 7 0.4129340959
## 8 0.0309662914
## 9 0.9628047372
## 10 0.0037460282
## 11 0.6602771084
## 12 0.2411799146
## 13 0.6283382054
## 14 0.5031664984
## 15 0.8029526548
## 16 1.0000000000
## 17 0.8913080527
## 18 0.1364235529
## 19 0.3476485575
## 20 0.1930549120
## 21 0.0101345317
## 22 0.1307609999
## 23 0.6381455557
## 24 0.0808567355
## 25 0.0107024688
## 26 0.5829826331
## 27 0.5476124188
## 28 0.1485320987
## 29 0.2157535073
## 30 0.4142404126
## 31 0.9229586931
## 32 0.0983619652
## 33 0.5804014350
## 34 0.4124475447
## 35 0.2351135572
## 36 0.0066664655
## 37 0.5203154060
## 38 0.4507561369
## 39 0.9450858318
## 40 0.3565028212
## 41 0.1786931909
## 42 0.5176461348
## 43 0.9912855978
## 44 0.0106680936
## 45 0.0236662735
## 46 1.0000000000
## 47 0.2351135572
## 48 1.0000000000
## 49 0.8928727963
## 50 0.0028934850
## 51 0.2088426439
## 52 0.0301141308
## 53 0.5600804138
## 54 0.7034031768
## 55 0.2379293712
## 56 0.7537812400
## 57 0.6636028946
## 58 0.9272823590
## 59 0.4139893461
## 60 0.8007330886
## 61 1.0000000000
## 62 0.2351135279
## 63 0.0106936618
## 64 1.0000000000
## 65 0.8077416187
## 66 0.0043176902
## 67 0.3774601841
## 68 0.2974122653
## 69 0.0561848343
## 70 1.0000000000
## 71 0.1560166642
## 72 1.0000000000
## 73 0.4615279288
## 74 1.0000000000
## 75 0.8963165707
## 76 0.5703526514
## 77 0.0208867779
## 78 0.0248226150
## 79 0.0739533680
## 80 0.2437832428
## 81 0.1764470127
## 82 1.0000000000
## 83 1.0000000000
## 84 1.0000000000
## 85 0.9531456025
## 86 1.0000000000
## 87 0.1254046574
## 88 0.6674720859
## 89 0.3474952582
## 90 0.0077802493
## 91 0.2375879109
## 92 0.0016020348
## 93 0.1223279929
## 94 0.0333643289
## 95 0.7244007264
## 96 0.1283890921
## 97 0.0202702592
## 98 0.1507955240
## 99 0.2900737553
## 100 0.0967109783
## 101 1.0000000000
## 102 1.0000000000
## 103 0.1853810060
## 104 0.3765042513
## 105 0.0903860628
## 106 0.7271960990
## 107 0.9036237895
## 108 0.0142038138
## 109 0.0225490113
## 110 0.9565571570
## 111 0.0618436715
## 112 0.6698387990
## 113 0.7355772826
## 114 0.1815403798
## 115 0.5066135176
## 116 0.0741112335
## 117 1.0000000000
## 118 0.6154787220
## 119 1.0000000000
## 120 0.0626960392
## 121 0.4056523573
## 122 0.3981978265
## 123 0.2497066194
## 124 0.9392480811
## 125 0.0049639617
## 126 0.1238610372
## 127 0.0701293072
## 128 0.0020907528
## 129 0.0220016304
## 130 0.2452443336
## 131 0.7296021134
## 132 1.0000000000
## 133 0.8910851234
## 134 0.9162610435
## 135 1.0000000000
## 136 0.4465474065
## 137 0.2905160106
## 138 0.1306257396
## 139 1.0000000000
## 140 0.9460726478
## 141 0.6217274277
## 142 0.0070547910
## 143 0.6727410196
## 144 0.7662842898
## 145 0.0157724846
## 146 0.0479136767
## 147 0.0627522949
## 148 0.0740992453
## 149 0.6711188628
## 150 0.0622770158
## 151 0.0141537612
## 152 0.5271164906
## 153 0.6735380998
## 154 0.0170337107
## 155 1.0000000000
## 156 0.0649787736
## 157 0.2139699987
## 158 0.0279421539
## 159 0.0903337814
## 160 0.9535133684
## 161 0.3454723568
## 162 0.2625349407
## 163 0.0062350224
## 164 0.2454687124
## 165 0.2508934441
## 166 0.2566701216
## 167 0.3758235301
## 168 0.2497801323
## 169 0.2216965949
## 170 0.2715932279
## 171 0.7986328926
## 172 0.7494069115
## 173 1.0000000000
## 174 0.9601257463
## 175 0.4244336910
## 176 0.0274861413
## 177 0.0864786471
## 178 1.0000000000
## 179 0.0104090271
## 180 0.2624272465
## 181 0.0070079844
## 182 0.2576192772
## 183 0.0020365491
## 184 1.0000000000
## 185 0.0020542347
## 186 0.2482200018
## 187 0.7153811214
## 188 0.2365789880
## 189 0.0368155949
## 190 0.3404824352
## 191 0.4777853297
## 192 1.0000000000
## 193 0.7661351139
## 194 0.0417142652
## 195 1.0000000000
## 196 0.0901508753
## 197 0.6843141916
## 198 0.0430355432
## 199 0.4177045651
## 200 0.3368463019
## 201 0.2326839120
## 202 0.1340474886
## 203 0.7743304441
## 204 0.6151254554
## 205 0.1947166979
## 206 0.5837266354
## 207 0.0166669568
## 208 0.1884040710
## 209 0.1801752549
## 210 0.3457829468
## 211 0.8262246725
## 212 0.7345399522
## 213 0.5339701013
## 214 0.3789681180
## 215 0.4792830385
## 216 1.0000000000
## 217 0.3516148359
## 218 0.8594343031
## 219 0.7880273589
## 220 0.9658832647
## 221 1.0000000000
## 222 0.0283301405
## 223 0.0334166247
## 224 0.6461328707
## 225 0.7267236316
## 226 1.0000000000
## 227 0.2410594331
## 228 0.2450647290
## 229 1.0000000000
## 230 0.9368532769
## 231 1.0000000000
## 232 0.2510439135
## 233 0.4755134190
## 234 0.2320589393
## 235 0.1505841821
## 236 0.1245526383
## 237 0.0841873686
## 238 0.2376082047
## 239 1.0000000000
## 240 0.0956638465
## 241 0.1144094955
## 242 0.3285664397
## 243 0.5176698605
## 244 0.0294285612
## 245 0.8365409769
## 246 1.0000000000
## 247 0.0049261206
## 248 0.1180380137
## 249 1.0000000000
## 250 1.0000000000
## 251 0.0751473886
## 252 0.0011700077
## 253 0.0636741684
## 254 0.8355065060
## 255 1.0000000000
## 256 0.0979582282
## 257 0.0095243673
## 258 0.0011233514
## 259 1.0000000000
## 260 0.8197608104
## 261 0.1392590271
## 262 1.0000000000
## 263 0.2298164248
## 264 0.8633864054
## 265 0.7403476123
## 266 0.0326340282
## 267 0.3507643511
## 268 0.2440254337
## 269 0.7778295775
## 270 0.0045959361
## 271 1.0000000000
## 272 0.4276326756
## 273 0.1042118914
## 274 0.3380105552
## 275 0.0308693830
## 276 0.1618342645
## 277 0.0739694540
## 278 0.0538829923
## 279 0.0579055339
## 280 0.0344200749
## 281 0.0193006307
## 282 0.6445098979
## 283 0.2506961732
## 284 0.2259422773
## 285 0.0239727751
## 286 0.8011204477
## 287 0.6700069553
## 288 0.0997503480
## 289 1.0000000000
## 290 0.0105846538
## 291 0.2351135572
## 292 0.4936632176
## 293 0.3963162771
## 294 0.2529510897
## 295 0.0343181782
## 296 0.3124076273
## 297 0.1470080448
## 298 0.5538036049
## 299 0.2546841046
## 300 0.1236118419
## 301 0.8804639441
## 302 0.2490920566
## 303 0.8455992580
## 304 0.5466069342
## 305 0.0295448126
## 306 0.6878508129
## 307 0.0193928114
## 308 0.3836036999
## 309 0.0759847473
## 310 0.9202335611
## 311 0.0065195498
## 312 0.0009636872
## 313 0.1143267122
## 314 0.4352799991
## 315 1.0000000000
## 316 0.1261795445
## 317 1.0000000000
## 318 0.8939014967
## 319 0.1246163310
## 320 0.0353528584
## 321 0.0118520219
## 322 0.4442409190
## 323 0.8183230056
## 324 0.0330242342
## 325 0.2775998424
## 326 0.3034871072
## 327 0.9756340680
## 328 0.1997650948
## 329 0.5959533903
## 330 0.7751898734
## 331 0.3788674778
## 332 0.0623017278
## 333 0.0287029257
## 334 0.2521288237
## 335 0.2438043275
## 336 0.3361509255
## 337 0.0749909326
## 338 0.1761831000
## 339 0.7264254592
##
## $artifacts$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] 339
##
## $summary$n_samples
## [1] 25
##
##
## $created_at
## [1] "2026-08-30 10:11:45 CST"
##
## $da_results
## logFC logCPM F PValue
## 1 0.30898235 13.77764 6.225506e-02 0.8029741404
## 2 -1.90613696 13.49367 1.881777e+00 0.1701777150
## 3 0.15892253 13.62763 1.202260e-02 0.9126920869
## 4 -0.92565436 13.61763 3.787353e-01 0.5466069277
## 5 -3.24154575 13.78463 4.951338e+00 0.0261032547
## 6 -1.86401277 13.78308 1.828533e+00 0.1763459652
## 7 1.06238803 13.71063 6.704197e-01 0.4129340959
## 8 -3.07214014 13.52167 4.656772e+00 0.0309662914
## 9 -0.05716276 13.47313 2.174914e-03 0.9628047372
## 10 -4.31005125 13.49738 8.408827e+00 0.0037460282
## 11 -0.58583386 13.49193 1.932042e-01 0.6602771084
## 12 -1.54697794 13.54854 1.373925e+00 0.2411799146
## 13 -0.62548534 13.61055 2.343423e-01 0.6283382054
## 14 -0.87364340 13.53510 4.482993e-01 0.5031664984
## 15 -0.31413049 13.74724 6.226893e-02 0.8029526548
## 16 0.00000000 13.53958 0.000000e+00 1.0000000000
## 17 -0.17357626 13.52712 1.867442e-02 0.8913080527
## 18 -1.87498088 13.67509 2.218369e+00 0.1364235529
## 19 1.18534653 13.58368 8.821441e-01 0.3476485575
## 20 1.73680048 13.64883 1.694486e+00 0.1930549120
## 21 3.76710384 13.63423 6.614807e+00 0.0101345317
## 22 -1.87544506 13.62591 2.284000e+00 0.1307609999
## 23 -0.61148315 13.40594 2.211956e-01 0.6381455557
## 24 -2.57488554 13.73203 3.048506e+00 0.0808567355
## 25 -3.80125603 13.66222 6.517674e+00 0.0107024688
## 26 0.71282463 13.64547 3.014664e-01 0.5829826331
## 27 -0.78187675 13.71333 3.616482e-01 0.5476124188
## 28 1.89913751 13.75141 2.087737e+00 0.1485320987
## 29 -1.84011337 13.69283 1.532680e+00 0.2157535073
## 30 -1.03728143 13.84318 6.666794e-01 0.4142404126
## 31 0.11485914 13.98842 9.353034e-03 0.9229586931
## 32 -2.34166108 13.90132 2.732656e+00 0.0983619652
## 33 0.67985803 13.83413 3.056155e-01 0.5804014350
## 34 -1.06136849 13.89741 6.718173e-01 0.4124475447
## 35 -1.66143087 13.69066 1.552877e+00 0.2351135572
## 36 -4.13384976 13.71524 7.365245e+00 0.0066664655
## 37 -0.85205264 13.51053 4.133111e-01 0.5203154060
## 38 -1.21338675 13.71454 5.688156e-01 0.4507561369
## 39 0.08621122 13.95960 4.744686e-03 0.9450858318
## 40 1.21039289 13.57501 8.502911e-01 0.3565028212
## 41 -1.87631286 13.57379 1.808834e+00 0.1786931909
## 42 -0.85478210 13.49017 4.186244e-01 0.5176461348
## 43 0.01465867 13.44670 1.193011e-04 0.9912855978
## 44 -3.62386677 13.45089 6.523401e+00 0.0106680936
## 45 -3.27942632 13.86024 5.121236e+00 0.0236662735
## 46 0.00000000 13.68601 0.000000e+00 1.0000000000
## 47 -1.65870438 13.56415 1.659694e+00 0.2351135572
## 48 0.00000000 13.51161 0.000000e+00 1.0000000000
## 49 0.16879868 13.78403 1.813737e-02 0.8928727963
## 50 -4.54499493 13.93165 8.879910e+00 0.0028934850
## 51 -1.72881523 13.67884 1.579732e+00 0.2088426439
## 52 -2.99117604 13.55100 4.704744e+00 0.0301141308
## 53 0.73513127 13.54483 3.395986e-01 0.5600804138
## 54 -0.48464491 13.46330 1.449680e-01 0.7034031768
## 55 -1.31566023 13.52143 1.393066e+00 0.2379293712
## 56 -0.40706079 13.40735 9.838895e-02 0.7537812400
## 57 0.56941687 13.47965 1.891931e-01 0.6636028946
## 58 0.10734614 13.95586 8.329844e-03 0.9272823590
## 59 -1.07940089 13.60238 6.673969e-01 0.4139893461
## 60 -0.32011331 13.44084 6.370998e-02 0.8007330886
## 61 0.00000000 13.68436 0.000000e+00 1.0000000000
## 62 -1.31557447 13.45526 1.431467e+00 0.2351135279
## 63 -3.77870434 13.64829 6.519140e+00 0.0106936618
## 64 0.00000000 13.50328 0.000000e+00 1.0000000000
## 65 -0.30830967 13.88128 5.921923e-02 0.8077416187
## 66 -4.39687316 13.71923 8.150628e+00 0.0043176902
## 67 -1.25109619 13.63437 7.790596e-01 0.3774601841
## 68 -1.41187505 13.44026 1.085928e+00 0.2974122653
## 69 2.56514727 13.46614 3.647819e+00 0.0561848343
## 70 0.00000000 13.64507 0.000000e+00 1.0000000000
## 71 -1.88872886 13.51332 2.012863e+00 0.1560166642
## 72 0.00000000 13.38681 0.000000e+00 1.0000000000
## 73 -0.96654043 13.60197 5.422483e-01 0.4615279288
## 74 0.00000000 13.71862 0.000000e+00 1.0000000000
## 75 0.16277509 13.61710 1.698348e-02 0.8963165707
## 76 -0.69648377 13.87234 3.221242e-01 0.5703526514
## 77 -3.37078919 13.61016 5.338709e+00 0.0208867779
## 78 -3.22936219 13.58885 5.038461e+00 0.0248226150
## 79 -2.42722965 13.66979 3.194005e+00 0.0739533680
## 80 -1.31543074 13.63071 1.358819e+00 0.2437832428
## 81 -1.87717763 13.80478 1.827679e+00 0.1764470127
## 82 0.00000000 13.58349 0.000000e+00 1.0000000000
## 83 0.00000000 13.62845 0.000000e+00 1.0000000000
## 84 0.00000000 13.53978 0.000000e+00 1.0000000000
## 85 -0.07191857 13.44069 3.452649e-03 0.9531456025
## 86 0.00000000 13.59596 0.000000e+00 1.0000000000
## 87 1.99703003 13.58198 2.349067e+00 0.1254046574
## 88 0.55439741 13.66428 1.845895e-01 0.6674720859
## 89 1.22419294 13.64753 8.827053e-01 0.3474952582
## 90 -3.85981770 13.55334 7.087596e+00 0.0077802493
## 91 -1.31566847 13.58517 1.395095e+00 0.2375879109
## 92 4.76235760 13.50817 9.965458e+00 0.0016020348
## 93 -1.99688181 13.66296 2.387855e+00 0.1223279929
## 94 2.91666287 13.41743 4.528832e+00 0.0333643289
## 95 -0.44269116 13.54200 1.243254e-01 0.7244007264
## 96 2.01599814 13.51948 2.312440e+00 0.1283890921
## 97 -3.26906121 13.53785 5.391008e+00 0.0202702592
## 98 1.72594265 13.63702 2.064652e+00 0.1507955240
## 99 -1.47202418 13.66303 1.119454e+00 0.2900737553
## 100 2.22320707 13.45012 2.759727e+00 0.0967109783
## 101 0.00000000 13.43539 0.000000e+00 1.0000000000
## 102 0.00000000 13.50409 0.000000e+00 1.0000000000
## 103 -1.74832915 13.81033 1.754306e+00 0.1853810060
## 104 -1.31579799 13.71033 7.821877e-01 0.3765042513
## 105 -2.36688818 13.53328 2.868302e+00 0.0903860628
## 106 0.43885833 13.55685 1.217118e-01 0.7271960990
## 107 -0.14745731 13.81156 1.466265e-02 0.9036237895
## 108 -3.49895858 13.55544 6.015744e+00 0.0142038138
## 109 -3.26288360 13.52032 5.205298e+00 0.0225490113
## 110 0.10161259 13.68506 6.186252e-03 0.9565571570
## 111 -2.58094758 13.43912 3.488393e+00 0.0618436715
## 112 -0.57776211 13.68886 1.818066e-01 0.6698387990
## 113 0.43808689 13.51600 1.140614e-01 0.7355772826
## 114 1.71957217 13.76278 1.785335e+00 0.1815403798
## 115 -0.85526212 13.59583 4.411022e-01 0.5066135176
## 116 -2.57412262 13.74069 3.190518e+00 0.0741112335
## 117 0.00000000 13.49479 0.000000e+00 1.0000000000
## 118 0.65636076 13.61012 2.522969e-01 0.6154787220
## 119 0.00000000 13.51832 0.000000e+00 1.0000000000
## 120 -2.57592246 13.42295 3.465731e+00 0.0626960392
## 121 1.05547040 13.52387 6.915930e-01 0.4056523573
## 122 -1.13741989 13.78688 7.138520e-01 0.3981978265
## 123 -1.53977902 13.45767 1.325172e+00 0.2497066194
## 124 -0.13789659 13.47804 5.809151e-03 0.9392480811
## 125 -3.94764725 13.39424 7.897700e+00 0.0049639617
## 126 -2.20652700 14.13848 2.368394e+00 0.1238610372
## 127 2.46901875 13.51993 3.281027e+00 0.0701293072
## 128 4.56302252 13.45845 9.475418e+00 0.0020907528
## 129 -3.20468825 13.56003 5.248073e+00 0.0220016304
## 130 -1.24873513 13.54404 1.350427e+00 0.2452443336
## 131 -0.43051228 13.42631 1.194871e-01 0.7296021134
## 132 0.00000000 13.63423 0.000000e+00 1.0000000000
## 133 -0.17286653 13.74265 1.875158e-02 0.8910851234
## 134 0.12891467 13.50509 1.105622e-02 0.9162610435
## 135 0.00000000 14.04518 0.000000e+00 1.0000000000
## 136 -1.00100355 13.43201 5.794680e-01 0.4465474065
## 137 -1.42273680 13.56908 1.117403e+00 0.2905160106
## 138 -1.94625441 13.73399 2.285606e+00 0.1306257396
## 139 0.00000000 13.55136 0.000000e+00 1.0000000000
## 140 0.03804163 13.56195 4.575435e-03 0.9460726478
## 141 -0.65719989 13.86171 2.434695e-01 0.6217274277
## 142 -3.94949512 13.59318 7.263389e+00 0.0070547910
## 143 0.54143801 13.50619 1.784281e-01 0.6727410196
## 144 -0.37406772 13.51319 8.835793e-02 0.7662842898
## 145 -3.52769161 13.64231 5.830998e+00 0.0157724846
## 146 -2.82522997 13.58344 3.914429e+00 0.0479136767
## 147 -2.71355433 13.80321 3.464247e+00 0.0627522949
## 148 -2.40752868 13.65672 3.190782e+00 0.0740992453
## 149 -0.52654232 13.82271 1.803118e-01 0.6711188628
## 150 -2.66984684 13.69927 3.476830e+00 0.0622770158
## 151 -3.51757414 13.52578 6.021980e+00 0.0141537612
## 152 -0.82345512 13.61441 3.999886e-01 0.5271164906
## 153 -0.56923983 13.67875 1.775067e-01 0.6735380998
## 154 3.40505697 13.52226 5.695708e+00 0.0170337107
## 155 0.00000000 13.50153 0.000000e+00 1.0000000000
## 156 -2.44172064 13.48247 3.406623e+00 0.0649787736
## 157 1.61864051 13.41433 1.544650e+00 0.2139699987
## 158 3.12035816 13.66797 4.833711e+00 0.0279421539
## 159 -2.38990623 13.54292 2.869234e+00 0.0903337814
## 160 -0.07031125 13.41277 3.398600e-03 0.9535133684
## 161 -1.24983497 13.64195 8.901423e-01 0.3454723568
## 162 -1.56940752 13.77526 1.255549e+00 0.2625349407
## 163 -4.06143494 13.88829 7.485774e+00 0.0062350224
## 164 -1.33698648 13.86218 1.349144e+00 0.2454687124
## 165 -1.33662302 13.70645 1.318547e+00 0.2508934441
## 166 -1.45342750 13.84808 1.286846e+00 0.2566701216
## 167 -1.15138805 13.56118 7.844221e-01 0.3758235301
## 168 1.36865121 13.71953 1.324760e+00 0.2497801323
## 169 -1.69837784 13.51527 1.493630e+00 0.2216965949
## 170 -1.53955965 13.65593 1.208879e+00 0.2715932279
## 171 -0.31574511 13.88660 6.508969e-02 0.7986328926
## 172 -0.42048423 13.51247 1.020384e-01 0.7494069115
## 173 0.00000000 13.70794 0.000000e+00 1.0000000000
## 174 0.04392314 13.55632 2.499763e-03 0.9601257463
## 175 -1.07826692 13.59432 6.380833e-01 0.4244336910
## 176 -3.13185706 13.56699 4.862113e+00 0.0274861413
## 177 2.27767180 13.57786 2.939585e+00 0.0864786471
## 178 0.00000000 13.80222 0.000000e+00 1.0000000000
## 179 3.74153522 13.62608 6.567182e+00 0.0104090271
## 180 -1.25358047 13.94693 1.256116e+00 0.2624272465
## 181 -3.94954323 13.58928 7.275358e+00 0.0070079844
## 182 -1.52750117 13.42415 1.281721e+00 0.2576192772
## 183 4.53082669 13.45381 9.523683e+00 0.0020365491
## 184 0.00000000 13.64417 0.000000e+00 1.0000000000
## 185 -4.63677049 13.53305 9.507793e+00 0.0020542347
## 186 -1.33676194 13.75370 1.333524e+00 0.2482200018
## 187 0.45869398 13.56051 1.329725e-01 0.7153811214
## 188 -1.31571639 13.56373 1.401112e+00 0.2365789880
## 189 -2.90410496 13.57654 4.360645e+00 0.0368155949
## 190 -1.27732629 13.54894 9.087419e-01 0.3404824352
## 191 -0.91835231 13.47739 5.039700e-01 0.4777853297
## 192 0.00000000 13.80537 0.000000e+00 1.0000000000
## 193 -0.37464165 13.66993 8.847414e-02 0.7661351139
## 194 -2.77266134 13.48646 4.148335e+00 0.0417142652
## 195 0.00000000 13.83672 0.000000e+00 1.0000000000
## 196 2.30381078 13.52103 2.872497e+00 0.0901508753
## 197 -0.55783698 13.57134 1.653240e-01 0.6843141916
## 198 -2.76088809 13.51103 4.095544e+00 0.0430355432
## 199 1.03525315 13.60980 6.568446e-01 0.4177045651
## 200 -1.30842799 13.57503 9.225281e-01 0.3368463019
## 201 -1.65184282 13.50101 1.424634e+00 0.2326839120
## 202 -1.88158957 13.82907 2.245531e+00 0.1340474886
## 203 -0.36833045 13.72669 8.221213e-02 0.7743304441
## 204 0.62880398 13.58713 2.528018e-01 0.6151254554
## 205 1.69009583 13.58386 1.681897e+00 0.1947166979
## 206 0.67745905 13.81410 3.002774e-01 0.5837266354
## 207 3.43196492 13.52587 5.733955e+00 0.0166669568
## 208 -1.86358405 13.62816 1.730402e+00 0.1884040710
## 209 -1.86398470 13.66434 1.796548e+00 0.1801752549
## 210 1.21974017 13.54584 8.889966e-01 0.3457829468
## 211 -0.28938405 13.71904 4.820422e-02 0.8262246725
## 212 -0.42723803 13.57691 1.149933e-01 0.7345399522
## 213 0.80517251 13.46214 3.868702e-01 0.5339701013
## 214 -1.09000453 13.90578 7.741478e-01 0.3789681180
## 215 -0.91669965 13.64604 5.005496e-01 0.4792830385
## 216 0.00000000 13.49761 0.000000e+00 1.0000000000
## 217 -1.22950239 13.76248 8.677402e-01 0.3516148359
## 218 0.21528167 13.41378 3.136478e-02 0.8594343031
## 219 -0.35634244 13.52859 7.229845e-02 0.7880273589
## 220 0.04851715 13.57385 1.829581e-03 0.9658832647
## 221 0.00000000 13.42775 0.000000e+00 1.0000000000
## 222 -3.10072377 13.61755 4.809924e+00 0.0283301405
## 223 -3.01964678 13.56730 4.526150e+00 0.0334166247
## 224 -0.61908142 13.48547 2.108293e-01 0.6461328707
## 225 -0.42938460 13.87815 1.221514e-01 0.7267236316
## 226 0.00000000 13.40892 0.000000e+00 1.0000000000
## 227 -1.24837564 13.45634 1.374628e+00 0.2410594331
## 228 1.36727897 13.85833 1.351456e+00 0.2450647290
## 229 0.00000000 13.78537 0.000000e+00 1.0000000000
## 230 0.11215585 13.43765 6.277143e-03 0.9368532769
## 231 0.00000000 13.66657 0.000000e+00 1.0000000000
## 232 -1.31627095 13.75876 1.317710e+00 0.2510439135
## 233 -0.94889390 13.43024 5.091920e-01 0.4755134190
## 234 -1.63980828 13.46556 1.428453e+00 0.2320589393
## 235 -2.06859665 13.61061 2.066790e+00 0.1505841821
## 236 -2.05297191 13.39390 2.359702e+00 0.1245526383
## 237 -2.26582310 13.39949 2.983026e+00 0.0841873686
## 238 -1.31566623 13.58556 1.394975e+00 0.2376082047
## 239 0.00000000 13.69667 0.000000e+00 1.0000000000
## 240 2.20220727 13.56852 2.777159e+00 0.0956638465
## 241 -1.98075636 13.54303 2.492872e+00 0.1144094955
## 242 -1.32979840 13.46732 9.546773e-01 0.3285664397
## 243 -0.83548140 13.51974 4.185770e-01 0.5176698605
## 244 -3.21703776 13.69463 4.744376e+00 0.0294285612
## 245 0.26073661 13.68221 4.257120e-02 0.8365409769
## 246 0.00000000 13.46182 0.000000e+00 1.0000000000
## 247 -4.26410628 13.79930 7.911559e+00 0.0049261206
## 248 -1.94547626 13.55522 2.443783e+00 0.1180380137
## 249 0.00000000 13.77484 0.000000e+00 1.0000000000
## 250 0.00000000 13.69342 0.000000e+00 1.0000000000
## 251 -2.44165423 13.69297 3.167820e+00 0.0751473886
## 252 4.91547331 13.54614 1.054609e+01 0.0011700077
## 253 -2.47814678 13.58956 3.440127e+00 0.0636741684
## 254 -0.29480525 13.44809 4.311958e-02 0.8355065060
## 255 0.00000000 13.45952 0.000000e+00 1.0000000000
## 256 -2.20812283 13.58750 2.739230e+00 0.0979582282
## 257 -3.80536109 13.86087 6.725588e+00 0.0095243673
## 258 -5.07638464 13.79962 1.062144e+01 0.0011233514
## 259 0.00000000 13.67408 0.000000e+00 1.0000000000
## 260 0.29068958 13.58925 5.192085e-02 0.8197608104
## 261 -2.10012989 13.66979 2.186642e+00 0.1392590271
## 262 0.00000000 13.74541 0.000000e+00 1.0000000000
## 263 -1.63946007 13.89494 1.442257e+00 0.2298164248
## 264 -0.22152673 13.54468 2.960862e-02 0.8633864054
## 265 -0.44400099 13.49555 1.098303e-01 0.7403476123
## 266 -3.04233111 13.66067 4.566750e+00 0.0326340282
## 267 1.29247040 13.79312 8.708102e-01 0.3507643511
## 268 -1.33650441 13.65793 1.357424e+00 0.2440254337
## 269 -0.38261307 13.66642 7.961416e-02 0.7778295775
## 270 -4.16536238 13.47636 8.037301e+00 0.0045959361
## 271 0.00000000 13.85562 0.000000e+00 1.0000000000
## 272 -1.08680272 13.54191 6.293198e-01 0.4276326756
## 273 -1.98050063 13.41423 2.640581e+00 0.1042118914
## 274 1.20220549 13.56375 9.180922e-01 0.3380105552
## 275 3.08727262 13.75638 4.662158e+00 0.0308693830
## 276 -1.86908815 13.60569 1.957429e+00 0.1618342645
## 277 -2.43229100 13.76114 3.193650e+00 0.0739694540
## 278 -2.66067396 13.53443 3.717613e+00 0.0538829923
## 279 2.57782107 13.54565 3.597599e+00 0.0579055339
## 280 -2.91995836 13.60660 4.475521e+00 0.0344200749
## 281 -3.43359249 13.65082 5.476684e+00 0.0193006307
## 282 0.59981879 13.52173 2.129113e-01 0.6445098979
## 283 -1.33659833 13.69892 1.319646e+00 0.2506961732
## 284 -1.68095504 13.51466 1.466492e+00 0.2259422773
## 285 -3.21644667 13.52154 5.098893e+00 0.0239727751
## 286 0.26322545 13.84464 6.345723e-02 0.8011204477
## 287 -0.53787263 13.52760 1.816098e-01 0.6700069553
## 288 2.11590794 13.66685 2.710272e+00 0.0997503480
## 289 0.00000000 13.99319 0.000000e+00 1.0000000000
## 290 -3.70223008 13.48070 6.537382e+00 0.0105846538
## 291 -1.66080445 13.45793 1.693337e+00 0.2351135572
## 292 -0.91775849 13.47710 4.685829e-01 0.4936632176
## 293 -1.16353159 13.69881 7.195659e-01 0.3963162771
## 294 -1.48886730 13.41388 1.307153e+00 0.2529510897
## 295 -2.96470911 13.54063 4.480592e+00 0.0343181782
## 296 1.25972948 13.40038 1.020622e+00 0.3124076273
## 297 -2.12188549 13.69891 2.103506e+00 0.1470080448
## 298 -0.79677606 13.39035 3.505820e-01 0.5538036049
## 299 -1.24773542 13.64418 1.297645e+00 0.2546841046
## 300 -1.98010596 13.66039 2.371539e+00 0.1236118419
## 301 0.19144852 13.69050 2.261618e-02 0.8804639441
## 302 -1.24830749 13.60613 1.328617e+00 0.2490920566
## 303 0.27093470 13.50957 4.569560e-02 0.8455992580
## 304 -1.07384031 13.56723 5.068467e-01 0.5466069342
## 305 3.11675308 13.58036 4.737588e+00 0.0295448126
## 306 0.50426850 13.43894 1.614357e-01 0.6878508129
## 307 -3.45029759 13.85775 5.468350e+00 0.0193928114
## 308 -1.16017641 13.66652 7.592196e-01 0.3836036999
## 309 -2.55004334 13.75221 3.149722e+00 0.0759847473
## 310 0.13424667 13.58796 1.002867e-02 0.9202335611
## 311 -3.79270158 13.39403 7.405370e+00 0.0065195498
## 312 5.17376692 13.63839 1.090563e+01 0.0009636872
## 313 2.08788166 13.53486 2.494012e+00 0.1143267122
## 314 -1.05980083 13.59877 6.087661e-01 0.4352799991
## 315 0.00000000 13.70726 0.000000e+00 1.0000000000
## 316 -1.95865407 13.83024 2.339465e+00 0.1261795445
## 317 0.00000000 13.52662 0.000000e+00 1.0000000000
## 318 0.16558678 13.77083 1.778865e-02 0.8939014967
## 319 -1.87605343 13.47984 2.358904e+00 0.1246163310
## 320 -2.99579054 13.54417 4.429824e+00 0.0353528584
## 321 -3.61169447 13.56815 6.336298e+00 0.0118520219
## 322 -1.08244734 13.67284 5.853721e-01 0.4442409190
## 323 -0.30604063 13.71216 5.276730e-02 0.8183230056
## 324 -3.00272346 13.56970 4.546381e+00 0.0330242342
## 325 -1.53203979 13.65326 1.178992e+00 0.2775998424
## 326 -1.36066455 13.53968 1.058969e+00 0.3034871072
## 327 -0.01543818 13.62384 9.329385e-04 0.9756340680
## 328 -1.83011136 13.67637 1.644412e+00 0.1997650948
## 329 -0.68944662 13.45508 2.811690e-01 0.5959533903
## 330 -0.37171909 13.72996 8.156986e-02 0.7751898734
## 331 -1.19113831 13.67317 7.744748e-01 0.3788674778
## 332 -2.47809854 13.47457 3.476174e+00 0.0623017278
## 333 3.09751207 13.49352 4.787386e+00 0.0287029257
## 334 -1.24802971 13.62387 1.311693e+00 0.2521288237
## 335 1.57809424 13.49597 1.358698e+00 0.2438043275
## 336 -1.26845475 13.50243 9.251873e-01 0.3361509255
## 337 2.44475662 13.59264 3.171226e+00 0.0749909326
## 338 -1.80624811 13.56742 1.829912e+00 0.1761831000
## 339 -0.44342172 13.53989 1.224292e-01 0.7264254592
## FDR Nhood SpatialFDR contrast
## 1 1.0000000 1 1.0000000 Age1wk - Age4wk
## 2 0.5016543 2 0.5174654 Age1wk - Age4wk
## 3 1.0000000 3 1.0000000 Age1wk - Age4wk
## 4 0.8515624 4 0.8711589 Age1wk - Age4wk
## 5 0.2047089 5 0.2108180 Age1wk - Age4wk
## 6 0.5069113 6 0.5246127 Age1wk - Age4wk
## 7 0.7164668 7 0.7390460 Age1wk - Age4wk
## 8 0.2047089 8 0.2108180 Age1wk - Age4wk
## 9 1.0000000 9 1.0000000 Age1wk - Age4wk
## 10 0.1294448 10 0.1296490 Age1wk - Age4wk
## 11 0.9513726 11 0.9651099 Age1wk - Age4wk
## 12 0.5390922 12 0.5488093 Age1wk - Age4wk
## 13 0.9301601 13 0.9512893 Age1wk - Age4wk
## 14 0.8161409 14 0.8340011 Age1wk - Age4wk
## 15 1.0000000 15 1.0000000 Age1wk - Age4wk
## 16 1.0000000 16 1.0000000 Age1wk - Age4wk
## 17 1.0000000 17 1.0000000 Age1wk - Age4wk
## 18 0.4322204 18 0.4461411 Age1wk - Age4wk
## 19 0.6547381 19 0.6625748 Age1wk - Age4wk
## 20 0.5277872 20 0.5488093 Age1wk - Age4wk
## 21 0.1395437 21 0.1515522 Age1wk - Age4wk
## 22 0.4221712 22 0.4350017 Age1wk - Age4wk
## 23 0.9405711 23 0.9570125 Age1wk - Age4wk
## 24 0.3384004 24 0.3490185 Age1wk - Age4wk
## 25 0.1395437 25 0.1515522 Age1wk - Age4wk
## 26 0.8834077 26 0.9036704 Age1wk - Age4wk
## 27 0.8515624 27 0.8711589 Age1wk - Age4wk
## 28 0.4564257 28 0.4755424 Age1wk - Age4wk
## 29 0.5390922 29 0.5488093 Age1wk - Age4wk
## 30 0.7164668 30 0.7390460 Age1wk - Age4wk
## 31 1.0000000 31 1.0000000 Age1wk - Age4wk
## 32 0.3704967 32 0.3781165 Age1wk - Age4wk
## 33 0.8834077 33 0.9034535 Age1wk - Age4wk
## 34 0.7164668 34 0.7390460 Age1wk - Age4wk
## 35 0.5390922 35 0.5488093 Age1wk - Age4wk
## 36 0.1328652 36 0.1365070 Age1wk - Age4wk
## 37 0.8281076 37 0.8451428 Age1wk - Age4wk
## 38 0.7527405 38 0.7705335 Age1wk - Age4wk
## 39 1.0000000 39 1.0000000 Age1wk - Age4wk
## 40 0.6604069 40 0.6728621 Age1wk - Age4wk
## 41 0.5086131 41 0.5279530 Age1wk - Age4wk
## 42 0.8277834 42 0.8451428 Age1wk - Age4wk
## 43 1.0000000 43 1.0000000 Age1wk - Age4wk
## 44 0.1395437 44 0.1515522 Age1wk - Age4wk
## 45 0.2031693 45 0.2108180 Age1wk - Age4wk
## 46 1.0000000 46 1.0000000 Age1wk - Age4wk
## 47 0.5390922 47 0.5488093 Age1wk - Age4wk
## 48 1.0000000 48 1.0000000 Age1wk - Age4wk
## 49 1.0000000 49 1.0000000 Age1wk - Age4wk
## 50 0.1226114 50 0.1296490 Age1wk - Age4wk
## 51 0.5390922 51 0.5488093 Age1wk - Age4wk
## 52 0.2047089 52 0.2108180 Age1wk - Age4wk
## 53 0.8630330 53 0.8772666 Age1wk - Age4wk
## 54 0.9812909 54 0.9831615 Age1wk - Age4wk
## 55 0.5390922 55 0.5488093 Age1wk - Age4wk
## 56 1.0000000 56 0.9949737 Age1wk - Age4wk
## 57 0.9513726 57 0.9651099 Age1wk - Age4wk
## 58 1.0000000 58 1.0000000 Age1wk - Age4wk
## 59 0.7164668 59 0.7390460 Age1wk - Age4wk
## 60 1.0000000 60 1.0000000 Age1wk - Age4wk
## 61 1.0000000 61 1.0000000 Age1wk - Age4wk
## 62 0.5390922 62 0.5488093 Age1wk - Age4wk
## 63 0.1395437 63 0.1515522 Age1wk - Age4wk
## 64 1.0000000 64 1.0000000 Age1wk - Age4wk
## 65 1.0000000 65 1.0000000 Age1wk - Age4wk
## 66 0.1294448 66 0.1296490 Age1wk - Age4wk
## 67 0.6833521 67 0.6958646 Age1wk - Age4wk
## 68 0.5965844 68 0.6052819 Age1wk - Age4wk
## 69 0.2976040 69 0.2946432 Age1wk - Age4wk
## 70 1.0000000 70 1.0000000 Age1wk - Age4wk
## 71 0.4680500 71 0.4875123 Age1wk - Age4wk
## 72 1.0000000 72 1.0000000 Age1wk - Age4wk
## 73 0.7669508 73 0.7856152 Age1wk - Age4wk
## 74 1.0000000 74 1.0000000 Age1wk - Age4wk
## 75 1.0000000 75 1.0000000 Age1wk - Age4wk
## 76 0.8748848 76 0.8907601 Age1wk - Age4wk
## 77 0.1966838 77 0.2108180 Age1wk - Age4wk
## 78 0.2047089 78 0.2108180 Age1wk - Age4wk
## 79 0.3219854 79 0.3303003 Age1wk - Age4wk
## 80 0.5390922 80 0.5488093 Age1wk - Age4wk
## 81 0.5069113 81 0.5246127 Age1wk - Age4wk
## 82 1.0000000 82 1.0000000 Age1wk - Age4wk
## 83 1.0000000 83 1.0000000 Age1wk - Age4wk
## 84 1.0000000 84 1.0000000 Age1wk - Age4wk
## 85 1.0000000 85 1.0000000 Age1wk - Age4wk
## 86 1.0000000 86 1.0000000 Age1wk - Age4wk
## 87 0.4193614 87 0.4295266 Age1wk - Age4wk
## 88 0.9513726 88 0.9651099 Age1wk - Age4wk
## 89 0.6547381 89 0.6625748 Age1wk - Age4wk
## 90 0.1388160 90 0.1440254 Age1wk - Age4wk
## 91 0.5390922 91 0.5488093 Age1wk - Age4wk
## 92 0.1012522 92 0.1035243 Age1wk - Age4wk
## 93 0.4193614 93 0.4295266 Age1wk - Age4wk
## 94 0.2047089 94 0.2108180 Age1wk - Age4wk
## 95 0.9933137 95 0.9927464 Age1wk - Age4wk
## 96 0.4221712 96 0.4324996 Age1wk - Age4wk
## 97 0.1963319 97 0.2108180 Age1wk - Age4wk
## 98 0.4564257 98 0.4755424 Age1wk - Age4wk
## 99 0.5862198 99 0.5986355 Age1wk - Age4wk
## 100 0.3704967 100 0.3781165 Age1wk - Age4wk
## 101 1.0000000 101 1.0000000 Age1wk - Age4wk
## 102 1.0000000 102 1.0000000 Age1wk - Age4wk
## 103 0.5151161 103 0.5378106 Age1wk - Age4wk
## 104 0.6833521 104 0.6958646 Age1wk - Age4wk
## 105 0.3562892 105 0.3621768 Age1wk - Age4wk
## 106 0.9933137 106 0.9927464 Age1wk - Age4wk
## 107 1.0000000 107 1.0000000 Age1wk - Age4wk
## 108 0.1660377 108 0.1757241 Age1wk - Age4wk
## 109 0.2011609 109 0.2108180 Age1wk - Age4wk
## 110 1.0000000 110 1.0000000 Age1wk - Age4wk
## 111 0.3039004 111 0.3010781 Age1wk - Age4wk
## 112 0.9513726 112 0.9651099 Age1wk - Age4wk
## 113 0.9934689 113 0.9927464 Age1wk - Age4wk
## 114 0.5086131 114 0.5300257 Age1wk - Age4wk
## 115 0.8178190 115 0.8364714 Age1wk - Age4wk
## 116 0.3219854 116 0.3303003 Age1wk - Age4wk
## 117 1.0000000 117 1.0000000 Age1wk - Age4wk
## 118 0.9191510 118 0.9399306 Age1wk - Age4wk
## 119 1.0000000 119 1.0000000 Age1wk - Age4wk
## 120 0.3039004 120 0.3010781 Age1wk - Age4wk
## 121 0.7162299 121 0.7343263 Age1wk - Age4wk
## 122 0.7067490 122 0.7246676 Age1wk - Age4wk
## 123 0.5390922 123 0.5488093 Age1wk - Age4wk
## 124 1.0000000 124 1.0000000 Age1wk - Age4wk
## 125 0.1294448 125 0.1296490 Age1wk - Age4wk
## 126 0.4193614 126 0.4295266 Age1wk - Age4wk
## 127 0.3219854 127 0.3227886 Age1wk - Age4wk
## 128 0.1012522 128 0.1035243 Age1wk - Age4wk
## 129 0.2011609 129 0.2108180 Age1wk - Age4wk
## 130 0.5390922 130 0.5488093 Age1wk - Age4wk
## 131 0.9933137 131 0.9927464 Age1wk - Age4wk
## 132 1.0000000 132 1.0000000 Age1wk - Age4wk
## 133 1.0000000 133 1.0000000 Age1wk - Age4wk
## 134 1.0000000 134 1.0000000 Age1wk - Age4wk
## 135 1.0000000 135 1.0000000 Age1wk - Age4wk
## 136 0.7494038 136 0.7662373 Age1wk - Age4wk
## 137 0.5862198 137 0.5986355 Age1wk - Age4wk
## 138 0.4221712 138 0.4350017 Age1wk - Age4wk
## 139 1.0000000 139 1.0000000 Age1wk - Age4wk
## 140 1.0000000 140 1.0000000 Age1wk - Age4wk
## 141 0.9244105 141 0.9452524 Age1wk - Age4wk
## 142 0.1328652 142 0.1365070 Age1wk - Age4wk
## 143 0.9513726 143 0.9651099 Age1wk - Age4wk
## 144 1.0000000 144 1.0000000 Age1wk - Age4wk
## 145 0.1782291 145 0.1901915 Age1wk - Age4wk
## 146 0.2619796 146 0.2594111 Age1wk - Age4wk
## 147 0.3039004 147 0.3010781 Age1wk - Age4wk
## 148 0.3219854 148 0.3303003 Age1wk - Age4wk
## 149 0.9513726 149 0.9651099 Age1wk - Age4wk
## 150 0.3039004 150 0.3010781 Age1wk - Age4wk
## 151 0.1660377 151 0.1757241 Age1wk - Age4wk
## 152 0.8350116 152 0.8532802 Age1wk - Age4wk
## 153 0.9513726 153 0.9651099 Age1wk - Age4wk
## 154 0.1804509 154 0.1911862 Age1wk - Age4wk
## 155 1.0000000 155 1.0000000 Age1wk - Age4wk
## 156 0.3059417 156 0.3015523 Age1wk - Age4wk
## 157 0.5390922 157 0.5488093 Age1wk - Age4wk
## 158 0.2047089 158 0.2108180 Age1wk - Age4wk
## 159 0.3562892 159 0.3621768 Age1wk - Age4wk
## 160 1.0000000 160 1.0000000 Age1wk - Age4wk
## 161 0.6547381 161 0.6625748 Age1wk - Age4wk
## 162 0.5426789 162 0.5543823 Age1wk - Age4wk
## 163 0.1328652 163 0.1365070 Age1wk - Age4wk
## 164 0.5390922 164 0.5488093 Age1wk - Age4wk
## 165 0.5390922 165 0.5488093 Age1wk - Age4wk
## 166 0.5390922 166 0.5488093 Age1wk - Age4wk
## 167 0.6833521 167 0.6958646 Age1wk - Age4wk
## 168 0.5390922 168 0.5488093 Age1wk - Age4wk
## 169 0.5390922 169 0.5488093 Age1wk - Age4wk
## 170 0.5580006 170 0.5712136 Age1wk - Age4wk
## 171 1.0000000 171 1.0000000 Age1wk - Age4wk
## 172 1.0000000 172 0.9949737 Age1wk - Age4wk
## 173 1.0000000 173 1.0000000 Age1wk - Age4wk
## 174 1.0000000 174 1.0000000 Age1wk - Age4wk
## 175 0.7266819 175 0.7486393 Age1wk - Age4wk
## 176 0.2047089 176 0.2108180 Age1wk - Age4wk
## 177 0.3532080 177 0.3608202 Age1wk - Age4wk
## 178 1.0000000 178 1.0000000 Age1wk - Age4wk
## 179 0.1395437 179 0.1515522 Age1wk - Age4wk
## 180 0.5426789 180 0.5543823 Age1wk - Age4wk
## 181 0.1328652 181 0.1365070 Age1wk - Age4wk
## 182 0.5390922 182 0.5488093 Age1wk - Age4wk
## 183 0.1012522 183 0.1035243 Age1wk - Age4wk
## 184 1.0000000 184 1.0000000 Age1wk - Age4wk
## 185 0.1012522 185 0.1035243 Age1wk - Age4wk
## 186 0.5390922 186 0.5488093 Age1wk - Age4wk
## 187 0.9933137 187 0.9927464 Age1wk - Age4wk
## 188 0.5390922 188 0.5488093 Age1wk - Age4wk
## 189 0.2115337 189 0.2173355 Age1wk - Age4wk
## 190 0.6547381 190 0.6611470 Age1wk - Age4wk
## 191 0.7849128 191 0.8041576 Age1wk - Age4wk
## 192 1.0000000 192 1.0000000 Age1wk - Age4wk
## 193 1.0000000 193 1.0000000 Age1wk - Age4wk
## 194 0.2356856 194 0.2363220 Age1wk - Age4wk
## 195 1.0000000 195 1.0000000 Age1wk - Age4wk
## 196 0.3562892 196 0.3621768 Age1wk - Age4wk
## 197 0.9625830 197 0.9685744 Age1wk - Age4wk
## 198 0.2391647 198 0.2382813 Age1wk - Age4wk
## 199 0.7187911 199 0.7418921 Age1wk - Age4wk
## 200 0.6547381 200 0.6595244 Age1wk - Age4wk
## 201 0.5390922 201 0.5488093 Age1wk - Age4wk
## 202 0.4286990 202 0.4427614 Age1wk - Age4wk
## 203 1.0000000 203 1.0000000 Age1wk - Age4wk
## 204 0.9191510 204 0.9399306 Age1wk - Age4wk
## 205 0.5280717 205 0.5488093 Age1wk - Age4wk
## 206 0.8834077 206 0.9036704 Age1wk - Age4wk
## 207 0.1804509 207 0.1911862 Age1wk - Age4wk
## 208 0.5192600 208 0.5403206 Age1wk - Age4wk
## 209 0.5086131 209 0.5287291 Age1wk - Age4wk
## 210 0.6547381 210 0.6625748 Age1wk - Age4wk
## 211 1.0000000 211 1.0000000 Age1wk - Age4wk
## 212 0.9934689 212 0.9927464 Age1wk - Age4wk
## 213 0.8419343 213 0.8591986 Age1wk - Age4wk
## 214 0.6833521 214 0.6958646 Age1wk - Age4wk
## 215 0.7849128 215 0.8041576 Age1wk - Age4wk
## 216 1.0000000 216 1.0000000 Age1wk - Age4wk
## 217 0.6549309 217 0.6662429 Age1wk - Age4wk
## 218 1.0000000 218 1.0000000 Age1wk - Age4wk
## 219 1.0000000 219 1.0000000 Age1wk - Age4wk
## 220 1.0000000 220 1.0000000 Age1wk - Age4wk
## 221 1.0000000 221 1.0000000 Age1wk - Age4wk
## 222 0.2047089 222 0.2108180 Age1wk - Age4wk
## 223 0.2047089 223 0.2108180 Age1wk - Age4wk
## 224 0.9441338 224 0.9600572 Age1wk - Age4wk
## 225 0.9933137 225 0.9927464 Age1wk - Age4wk
## 226 1.0000000 226 1.0000000 Age1wk - Age4wk
## 227 0.5390922 227 0.5488093 Age1wk - Age4wk
## 228 0.5390922 228 0.5488093 Age1wk - Age4wk
## 229 1.0000000 229 1.0000000 Age1wk - Age4wk
## 230 1.0000000 230 1.0000000 Age1wk - Age4wk
## 231 1.0000000 231 1.0000000 Age1wk - Age4wk
## 232 0.5390922 232 0.5488093 Age1wk - Age4wk
## 233 0.7849128 233 0.8041576 Age1wk - Age4wk
## 234 0.5390922 234 0.5488093 Age1wk - Age4wk
## 235 0.4564257 235 0.4755424 Age1wk - Age4wk
## 236 0.4193614 236 0.4295266 Age1wk - Age4wk
## 237 0.3480429 237 0.3537779 Age1wk - Age4wk
## 238 0.5390922 238 0.5488093 Age1wk - Age4wk
## 239 1.0000000 239 1.0000000 Age1wk - Age4wk
## 240 0.3704967 240 0.3779342 Age1wk - Age4wk
## 241 0.4126045 241 0.4230634 Age1wk - Age4wk
## 242 0.6475815 242 0.6531982 Age1wk - Age4wk
## 243 0.8277834 243 0.8451428 Age1wk - Age4wk
## 244 0.2047089 244 0.2108180 Age1wk - Age4wk
## 245 1.0000000 245 1.0000000 Age1wk - Age4wk
## 246 1.0000000 246 1.0000000 Age1wk - Age4wk
## 247 0.1294448 247 0.1296490 Age1wk - Age4wk
## 248 0.4193614 248 0.4295266 Age1wk - Age4wk
## 249 1.0000000 249 1.0000000 Age1wk - Age4wk
## 250 1.0000000 250 1.0000000 Age1wk - Age4wk
## 251 0.3219854 251 0.3303003 Age1wk - Age4wk
## 252 0.1012522 252 0.1035243 Age1wk - Age4wk
## 253 0.3040217 253 0.3010781 Age1wk - Age4wk
## 254 1.0000000 254 1.0000000 Age1wk - Age4wk
## 255 1.0000000 255 1.0000000 Age1wk - Age4wk
## 256 0.3704967 256 0.3781165 Age1wk - Age4wk
## 257 0.1395437 257 0.1515522 Age1wk - Age4wk
## 258 0.1012522 258 0.1035243 Age1wk - Age4wk
## 259 1.0000000 259 1.0000000 Age1wk - Age4wk
## 260 1.0000000 260 1.0000000 Age1wk - Age4wk
## 261 0.4371186 261 0.4523858 Age1wk - Age4wk
## 262 1.0000000 262 1.0000000 Age1wk - Age4wk
## 263 0.5390922 263 0.5488093 Age1wk - Age4wk
## 264 1.0000000 264 1.0000000 Age1wk - Age4wk
## 265 0.9959438 265 0.9949737 Age1wk - Age4wk
## 266 0.2047089 266 0.2108180 Age1wk - Age4wk
## 267 0.6549309 267 0.6662429 Age1wk - Age4wk
## 268 0.5390922 268 0.5488093 Age1wk - Age4wk
## 269 1.0000000 269 1.0000000 Age1wk - Age4wk
## 270 0.1294448 270 0.1296490 Age1wk - Age4wk
## 271 1.0000000 271 1.0000000 Age1wk - Age4wk
## 272 0.7284798 272 0.7486393 Age1wk - Age4wk
## 273 0.3839982 273 0.3939420 Age1wk - Age4wk
## 274 0.6547381 274 0.6595244 Age1wk - Age4wk
## 275 0.2047089 275 0.2108180 Age1wk - Age4wk
## 276 0.4812440 276 0.5001279 Age1wk - Age4wk
## 277 0.3219854 277 0.3303003 Age1wk - Age4wk
## 278 0.2899418 278 0.2874111 Age1wk - Age4wk
## 279 0.3019996 279 0.3007969 Age1wk - Age4wk
## 280 0.2047089 280 0.2108180 Age1wk - Age4wk
## 281 0.1933577 281 0.2092038 Age1wk - Age4wk
## 282 0.9441338 282 0.9600572 Age1wk - Age4wk
## 283 0.5390922 283 0.5488093 Age1wk - Age4wk
## 284 0.5390922 284 0.5488093 Age1wk - Age4wk
## 285 0.2031693 285 0.2108180 Age1wk - Age4wk
## 286 1.0000000 286 1.0000000 Age1wk - Age4wk
## 287 0.9513726 287 0.9651099 Age1wk - Age4wk
## 288 0.3715975 288 0.3815324 Age1wk - Age4wk
## 289 1.0000000 289 1.0000000 Age1wk - Age4wk
## 290 0.1395437 290 0.1515522 Age1wk - Age4wk
## 291 0.5390922 291 0.5488093 Age1wk - Age4wk
## 292 0.8045761 292 0.8229023 Age1wk - Age4wk
## 293 0.7067490 293 0.7228042 Age1wk - Age4wk
## 294 0.5390922 294 0.5488093 Age1wk - Age4wk
## 295 0.2047089 295 0.2108180 Age1wk - Age4wk
## 296 0.6193344 296 0.6251441 Age1wk - Age4wk
## 297 0.4564257 297 0.4745536 Age1wk - Age4wk
## 298 0.8572576 298 0.8711589 Age1wk - Age4wk
## 299 0.5390922 299 0.5488093 Age1wk - Age4wk
## 300 0.4193614 300 0.4295266 Age1wk - Age4wk
## 301 1.0000000 301 1.0000000 Age1wk - Age4wk
## 302 0.5390922 302 0.5488093 Age1wk - Age4wk
## 303 1.0000000 303 1.0000000 Age1wk - Age4wk
## 304 0.8515624 304 0.8711589 Age1wk - Age4wk
## 305 0.2047089 305 0.2108180 Age1wk - Age4wk
## 306 0.9635596 306 0.9685744 Age1wk - Age4wk
## 307 0.1933577 307 0.2092038 Age1wk - Age4wk
## 308 0.6880511 308 0.7019225 Age1wk - Age4wk
## 309 0.3219854 309 0.3315943 Age1wk - Age4wk
## 310 1.0000000 310 1.0000000 Age1wk - Age4wk
## 311 0.1328652 311 0.1365070 Age1wk - Age4wk
## 312 0.1012522 312 0.1035243 Age1wk - Age4wk
## 313 0.4126045 313 0.4230634 Age1wk - Age4wk
## 314 0.7377996 314 0.7593725 Age1wk - Age4wk
## 315 1.0000000 315 1.0000000 Age1wk - Age4wk
## 316 0.4193614 316 0.4295266 Age1wk - Age4wk
## 317 1.0000000 317 1.0000000 Age1wk - Age4wk
## 318 1.0000000 318 1.0000000 Age1wk - Age4wk
## 319 0.4193614 319 0.4295266 Age1wk - Age4wk
## 320 0.2066314 320 0.2126535 Age1wk - Age4wk
## 321 0.1488087 321 0.1622165 Age1wk - Age4wk
## 322 0.7492421 322 0.7662373 Age1wk - Age4wk
## 323 1.0000000 323 1.0000000 Age1wk - Age4wk
## 324 0.2047089 324 0.2108180 Age1wk - Age4wk
## 325 0.5669057 325 0.5787362 Age1wk - Age4wk
## 326 0.6051890 326 0.6106283 Age1wk - Age4wk
## 327 1.0000000 327 1.0000000 Age1wk - Age4wk
## 328 0.5374632 328 0.5488093 Age1wk - Age4wk
## 329 0.8979031 329 0.9151157 Age1wk - Age4wk
## 330 1.0000000 330 1.0000000 Age1wk - Age4wk
## 331 0.6833521 331 0.6958646 Age1wk - Age4wk
## 332 0.3039004 332 0.3010781 Age1wk - Age4wk
## 333 0.2047089 333 0.2108180 Age1wk - Age4wk
## 334 0.5390922 334 0.5488093 Age1wk - Age4wk
## 335 0.5390922 335 0.5488093 Age1wk - Age4wk
## 336 0.6547381 336 0.6595244 Age1wk - Age4wk
## 337 0.3219854 337 0.3303003 Age1wk - Age4wk
## 338 0.5069113 338 0.5246127 Age1wk - Age4wk
## 339 0.9933137 339 0.9927464 Age1wk - Age4wk
## PValue_adj_withinNhood
## 1 0.8029741404
## 2 0.1701777150
## 3 0.9126920869
## 4 0.5466069277
## 5 0.0261032547
## 6 0.1763459652
## 7 0.4129340959
## 8 0.0309662914
## 9 0.9628047372
## 10 0.0037460282
## 11 0.6602771084
## 12 0.2411799146
## 13 0.6283382054
## 14 0.5031664984
## 15 0.8029526548
## 16 1.0000000000
## 17 0.8913080527
## 18 0.1364235529
## 19 0.3476485575
## 20 0.1930549120
## 21 0.0101345317
## 22 0.1307609999
## 23 0.6381455557
## 24 0.0808567355
## 25 0.0107024688
## 26 0.5829826331
## 27 0.5476124188
## 28 0.1485320987
## 29 0.2157535073
## 30 0.4142404126
## 31 0.9229586931
## 32 0.0983619652
## 33 0.5804014350
## 34 0.4124475447
## 35 0.2351135572
## 36 0.0066664655
## 37 0.5203154060
## 38 0.4507561369
## 39 0.9450858318
## 40 0.3565028212
## 41 0.1786931909
## 42 0.5176461348
## 43 0.9912855978
## 44 0.0106680936
## 45 0.0236662735
## 46 1.0000000000
## 47 0.2351135572
## 48 1.0000000000
## 49 0.8928727963
## 50 0.0028934850
## 51 0.2088426439
## 52 0.0301141308
## 53 0.5600804138
## 54 0.7034031768
## 55 0.2379293712
## 56 0.7537812400
## 57 0.6636028946
## 58 0.9272823590
## 59 0.4139893461
## 60 0.8007330886
## 61 1.0000000000
## 62 0.2351135279
## 63 0.0106936618
## 64 1.0000000000
## 65 0.8077416187
## 66 0.0043176902
## 67 0.3774601841
## 68 0.2974122653
## 69 0.0561848343
## 70 1.0000000000
## 71 0.1560166642
## 72 1.0000000000
## 73 0.4615279288
## 74 1.0000000000
## 75 0.8963165707
## 76 0.5703526514
## 77 0.0208867779
## 78 0.0248226150
## 79 0.0739533680
## 80 0.2437832428
## 81 0.1764470127
## 82 1.0000000000
## 83 1.0000000000
## 84 1.0000000000
## 85 0.9531456025
## 86 1.0000000000
## 87 0.1254046574
## 88 0.6674720859
## 89 0.3474952582
## 90 0.0077802493
## 91 0.2375879109
## 92 0.0016020348
## 93 0.1223279929
## 94 0.0333643289
## 95 0.7244007264
## 96 0.1283890921
## 97 0.0202702592
## 98 0.1507955240
## 99 0.2900737553
## 100 0.0967109783
## 101 1.0000000000
## 102 1.0000000000
## 103 0.1853810060
## 104 0.3765042513
## 105 0.0903860628
## 106 0.7271960990
## 107 0.9036237895
## 108 0.0142038138
## 109 0.0225490113
## 110 0.9565571570
## 111 0.0618436715
## 112 0.6698387990
## 113 0.7355772826
## 114 0.1815403798
## 115 0.5066135176
## 116 0.0741112335
## 117 1.0000000000
## 118 0.6154787220
## 119 1.0000000000
## 120 0.0626960392
## 121 0.4056523573
## 122 0.3981978265
## 123 0.2497066194
## 124 0.9392480811
## 125 0.0049639617
## 126 0.1238610372
## 127 0.0701293072
## 128 0.0020907528
## 129 0.0220016304
## 130 0.2452443336
## 131 0.7296021134
## 132 1.0000000000
## 133 0.8910851234
## 134 0.9162610435
## 135 1.0000000000
## 136 0.4465474065
## 137 0.2905160106
## 138 0.1306257396
## 139 1.0000000000
## 140 0.9460726478
## 141 0.6217274277
## 142 0.0070547910
## 143 0.6727410196
## 144 0.7662842898
## 145 0.0157724846
## 146 0.0479136767
## 147 0.0627522949
## 148 0.0740992453
## 149 0.6711188628
## 150 0.0622770158
## 151 0.0141537612
## 152 0.5271164906
## 153 0.6735380998
## 154 0.0170337107
## 155 1.0000000000
## 156 0.0649787736
## 157 0.2139699987
## 158 0.0279421539
## 159 0.0903337814
## 160 0.9535133684
## 161 0.3454723568
## 162 0.2625349407
## 163 0.0062350224
## 164 0.2454687124
## 165 0.2508934441
## 166 0.2566701216
## 167 0.3758235301
## 168 0.2497801323
## 169 0.2216965949
## 170 0.2715932279
## 171 0.7986328926
## 172 0.7494069115
## 173 1.0000000000
## 174 0.9601257463
## 175 0.4244336910
## 176 0.0274861413
## 177 0.0864786471
## 178 1.0000000000
## 179 0.0104090271
## 180 0.2624272465
## 181 0.0070079844
## 182 0.2576192772
## 183 0.0020365491
## 184 1.0000000000
## 185 0.0020542347
## 186 0.2482200018
## 187 0.7153811214
## 188 0.2365789880
## 189 0.0368155949
## 190 0.3404824352
## 191 0.4777853297
## 192 1.0000000000
## 193 0.7661351139
## 194 0.0417142652
## 195 1.0000000000
## 196 0.0901508753
## 197 0.6843141916
## 198 0.0430355432
## 199 0.4177045651
## 200 0.3368463019
## 201 0.2326839120
## 202 0.1340474886
## 203 0.7743304441
## 204 0.6151254554
## 205 0.1947166979
## 206 0.5837266354
## 207 0.0166669568
## 208 0.1884040710
## 209 0.1801752549
## 210 0.3457829468
## 211 0.8262246725
## 212 0.7345399522
## 213 0.5339701013
## 214 0.3789681180
## 215 0.4792830385
## 216 1.0000000000
## 217 0.3516148359
## 218 0.8594343031
## 219 0.7880273589
## 220 0.9658832647
## 221 1.0000000000
## 222 0.0283301405
## 223 0.0334166247
## 224 0.6461328707
## 225 0.7267236316
## 226 1.0000000000
## 227 0.2410594331
## 228 0.2450647290
## 229 1.0000000000
## 230 0.9368532769
## 231 1.0000000000
## 232 0.2510439135
## 233 0.4755134190
## 234 0.2320589393
## 235 0.1505841821
## 236 0.1245526383
## 237 0.0841873686
## 238 0.2376082047
## 239 1.0000000000
## 240 0.0956638465
## 241 0.1144094955
## 242 0.3285664397
## 243 0.5176698605
## 244 0.0294285612
## 245 0.8365409769
## 246 1.0000000000
## 247 0.0049261206
## 248 0.1180380137
## 249 1.0000000000
## 250 1.0000000000
## 251 0.0751473886
## 252 0.0011700077
## 253 0.0636741684
## 254 0.8355065060
## 255 1.0000000000
## 256 0.0979582282
## 257 0.0095243673
## 258 0.0011233514
## 259 1.0000000000
## 260 0.8197608104
## 261 0.1392590271
## 262 1.0000000000
## 263 0.2298164248
## 264 0.8633864054
## 265 0.7403476123
## 266 0.0326340282
## 267 0.3507643511
## 268 0.2440254337
## 269 0.7778295775
## 270 0.0045959361
## 271 1.0000000000
## 272 0.4276326756
## 273 0.1042118914
## 274 0.3380105552
## 275 0.0308693830
## 276 0.1618342645
## 277 0.0739694540
## 278 0.0538829923
## 279 0.0579055339
## 280 0.0344200749
## 281 0.0193006307
## 282 0.6445098979
## 283 0.2506961732
## 284 0.2259422773
## 285 0.0239727751
## 286 0.8011204477
## 287 0.6700069553
## 288 0.0997503480
## 289 1.0000000000
## 290 0.0105846538
## 291 0.2351135572
## 292 0.4936632176
## 293 0.3963162771
## 294 0.2529510897
## 295 0.0343181782
## 296 0.3124076273
## 297 0.1470080448
## 298 0.5538036049
## 299 0.2546841046
## 300 0.1236118419
## 301 0.8804639441
## 302 0.2490920566
## 303 0.8455992580
## 304 0.5466069342
## 305 0.0295448126
## 306 0.6878508129
## 307 0.0193928114
## 308 0.3836036999
## 309 0.0759847473
## 310 0.9202335611
## 311 0.0065195498
## 312 0.0009636872
## 313 0.1143267122
## 314 0.4352799991
## 315 1.0000000000
## 316 0.1261795445
## 317 1.0000000000
## 318 0.8939014967
## 319 0.1246163310
## 320 0.0353528584
## 321 0.0118520219
## 322 0.4442409190
## 323 0.8183230056
## 324 0.0330242342
## 325 0.2775998424
## 326 0.3034871072
## 327 0.9756340680
## 328 0.1997650948
## 329 0.5959533903
## 330 0.7751898734
## 331 0.3788674778
## 332 0.0623017278
## 333 0.0287029257
## 334 0.2521288237
## 335 0.2438043275
## 336 0.3361509255
## 337 0.0749909326
## 338 0.1761831000
## 339 0.7264254592
##
## $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"
##
## $contrasts
## [1] "Age1wk - Age4wk"22.3 Multi-contrast testing
Use per_contrast = FALSE to fit one model and test multiple contrasts jointly. Use per_contrast = TRUE to run each contrast and stack results.
contrasts <- c(
"Age1wk - Age4wk",
"Age4wk - Age16wk",
"Age16wk - Age32wk",
"Age32wk - Age52wk"
)
res2 <- RunMilo(
sce = sce,
sample_col = "Sample",
condition_col = "Age",
name = "milo_multi",
contrasts = contrasts,
per_contrast = TRUE,
k1 = 11, k2 = 11, d1 = 40, d2 = 40, d3 = 40,
prop = 0.2,
refinement_scheme = "graph"
)
head(res2$da_results)## logFC logCPM F PValue FDR Nhood
## 1 0.3089824 13.77764 0.06225506 0.80297414 1.0000000 1
## 2 -1.9061370 13.49367 1.88177693 0.17017772 0.5016543 2
## 3 0.1589225 13.62763 0.01202260 0.91269209 1.0000000 3
## 4 -0.9256544 13.61763 0.37873529 0.54660693 0.8515624 4
## 5 -3.2415458 13.78463 4.95133825 0.02610325 0.2047089 5
## 6 -1.8640128 13.78308 1.82853346 0.17634597 0.5069113 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 1.0000000 Age1wk - Age4wk 0.9760593
## 2 0.5174654 Age1wk - Age4wk 0.4534587
## 3 1.0000000 Age1wk - Age4wk 0.9126921
## 4 0.8711589 Age1wk - Age4wk 0.5872073
## 5 0.2108180 Age1wk - Age4wk 0.1044130
## 6 0.5246127 Age1wk - Age4wk 0.705383922.4 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 1.19435140 11.11520 0.3290811 3.62935286 0.0002865953
## 2 -0.56168036 10.58540 0.3573794 -1.57166428 0.1160791753
## 3 -0.03097665 12.08108 0.3677873 -0.08422435 0.9328812064
## 4 -1.43869690 10.56466 0.4392623 -3.27525725 0.0010556604
## 5 0.04402348 11.02846 0.3081513 0.14286319 0.8864021939
## 6 0.37239926 11.89417 0.3563047 1.04517090 0.2959728097
## tenx_lane_variance Converged Logliklihood Nhood
## 1 0.00000001 TRUE 336.7219 1
## 2 0.01691159 FALSE 200.8855 2
## 3 0.00000001 TRUE 850.5434 3
## 4 1.92556215 FALSE 244.1509 4
## 5 0.00000001 TRUE 238.1128 5
## 6 0.09183497 FALSE 777.0794 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 0.002241052 adjmfc.timed0 high 0.0002865953
## 2 0.261372026 adjmfc.timed0 high 0.1160791753
## 3 0.958926664 adjmfc.timed0 high 0.9328812064
## 4 0.007276947 adjmfc.timed0 high 0.0010556604
## 5 0.933265549 adjmfc.timed0 high 0.8864021939
## 6 0.464927659 adjmfc.timed0 high 0.295972809722.5 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 1.19429853 11.11520 0.3367312 3.54674193 0.0003932516
## 2 -0.55629640 10.58540 0.3511482 -1.58422097 0.1131917705
## 3 -0.03094956 12.08108 0.3698435 -0.08368285 0.9333117590
## 4 -1.44891207 10.56466 0.4437223 -3.26535813 0.0010932595
## 5 0.04402317 11.02846 0.3081512 0.14286226 0.8864029299
## 6 0.34323159 11.89417 0.3530372 0.97222489 0.3309706577
## tenx_lane_variance Converged Logliklihood Nhood
## 1 0.00000001 TRUE 337.0783 1
## 2 0.02763260 FALSE 201.1437 2
## 3 0.00000001 TRUE 850.5353 3
## 4 2.18259985 FALSE 244.1253 4
## 5 0.00000001 TRUE 238.1128 5
## 6 0.10136612 FALSE 776.1873 6
## SpatialFDR
## 1 0.003083933
## 2 0.254683335
## 3 0.960374531
## 4 0.007536128
## 5 0.930135391
## 6 0.507159943