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)$PCAcolData(sce)containing a sample column and a condition column
UMAP is optional (used for visualization only).
22.2 Two-group DA (GLM)
colData(sce)$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 TRUE
## 360 6## logFC logCPM F PValue FDR Nhood
## 1 1.059354 13.68486 0.64752416 0.42102538 0.7190866 1
## 2 -2.377079 13.42732 3.08234940 0.07918794 0.3116429 2
## 3 -0.392660 13.60684 0.09235521 0.76121271 0.9835711 3
## 4 -2.120548 13.50604 2.46639853 0.11634736 0.3801544 4
## 5 -2.709153 13.58856 3.81911258 0.05070909 0.2410328 5
## 6 -1.530199 13.68581 1.21236993 0.27089947 0.5707173 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 0.7360658 Age1wk - Age4wk 0.42102538
## 2 0.3094980 Age1wk - Age4wk 0.07918794
## 3 0.9945429 Age1wk - Age4wk 0.76121271
## 4 0.3762469 Age1wk - Age4wk 0.11634736
## 5 0.2409513 Age1wk - Age4wk 0.05070909
## 6 0.5831511 Age1wk - Age4wk 0.27089947## $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 1.05935398 13.68486 6.475242e-01 0.4210253845
## 2 -2.37707947 13.42732 3.082349e+00 0.0791879438
## 3 -0.39265998 13.60684 9.235521e-02 0.7612127132
## 4 -2.12054771 13.50604 2.466399e+00 0.1163473638
## 5 -2.70915344 13.58856 3.819113e+00 0.0507090901
## 6 -1.53019896 13.68581 1.212370e+00 0.2708994749
## 7 1.09599128 13.59844 7.496791e-01 0.3866062173
## 8 -2.06475222 13.57967 2.419995e+00 0.1198385389
## 9 -0.04560136 13.39561 1.641395e-03 0.9676843442
## 10 -4.07040881 13.41032 8.278258e+00 0.0040238627
## 11 1.19921557 13.75236 1.276151e+00 0.2586529492
## 12 -1.29745201 13.46307 1.015897e+00 0.3135274330
## 13 -1.20542395 13.67260 1.256354e+00 0.2623791367
## 14 -0.98814968 13.43876 6.203899e-01 0.4309279424
## 15 0.20025829 13.75932 2.475198e-02 0.8749909807
## 16 0.00000000 13.69412 0.000000e+00 1.0000000000
## 17 -0.15379327 13.43376 1.565209e-02 0.9004412283
## 18 -1.31601366 13.46775 1.409391e+00 0.2387063266
## 19 1.21427610 13.50690 9.374195e-01 0.3329743580
## 20 2.43410452 13.70102 3.122870e+00 0.0772423580
## 21 1.77377154 13.56292 1.995813e+00 0.1577769278
## 22 -2.36844178 13.45807 3.423020e+00 0.0643335849
## 23 -1.14373521 13.68938 7.302067e-01 0.3928441499
## 24 2.23367648 13.66217 2.667019e+00 0.1024907363
## 25 -2.86408861 13.71473 3.886690e+00 0.0487078683
## 26 -3.72370108 13.53541 7.013553e+00 0.0081068544
## 27 0.07472994 13.32977 3.208742e-03 0.9975727284
## 28 -0.09909769 13.57336 6.102058e-03 0.9377381769
## 29 -0.55033324 13.45792 1.995491e-01 0.6550982620
## 30 -0.78270885 13.40775 3.243162e-01 0.5690427236
## 31 -1.16966589 13.41634 7.884905e-01 0.3745861439
## 32 -1.37930895 13.66319 9.950833e-01 0.3185361078
## 33 0.36089085 13.75338 7.327950e-02 0.7866279704
## 34 -0.40319522 13.63130 9.077072e-02 0.7632081809
## 35 0.32138321 13.39361 6.763359e-02 0.7948212664
## 36 -1.31810889 13.65063 1.346541e+00 0.2459215202
## 37 0.00000000 13.40337 0.000000e+00 1.0000000000
## 38 -3.03426791 13.44462 5.097626e+00 0.0239879511
## 39 -1.19464417 13.50121 8.380067e-01 0.3599976255
## 40 -2.02720474 13.97287 2.462967e+00 0.1166016755
## 41 0.43629119 13.74538 1.152589e-01 0.7342443136
## 42 -0.25488699 13.60452 3.914150e-02 0.8431740949
## 43 -0.60138790 13.41370 1.975954e-01 0.6566819714
## 44 -1.84607119 13.80389 1.921286e+00 0.1657571817
## 45 0.20265753 13.50395 2.435929e-02 0.8759785037
## 46 -2.26952397 13.61480 2.757547e+00 0.0968393657
## 47 -3.10981171 13.81099 5.135608e+00 0.0234689461
## 48 0.00000000 13.50189 0.000000e+00 1.0000000000
## 49 -0.71509629 13.65630 2.578243e-01 0.6116341342
## 50 0.00000000 13.39794 0.000000e+00 1.0000000000
## 51 -2.48176794 13.46753 3.277419e+00 0.0702802771
## 52 -2.41408221 13.42095 3.159020e+00 0.0755499959
## 53 -2.37451572 13.77219 2.821759e+00 0.0930371424
## 54 0.60905075 13.57182 2.433984e-01 0.6217770989
## 55 -0.29801955 13.39047 5.869954e-02 0.8085700929
## 56 -2.26965213 13.66149 3.031367e+00 0.0817112190
## 57 -1.04345900 13.43956 6.436609e-01 0.4224142763
## 58 -0.83291580 13.35944 4.207033e-01 0.5166066781
## 59 0.04185050 13.68751 1.546715e-03 0.9686297158
## 60 -1.00420273 13.56466 6.117322e-01 0.4341616628
## 61 0.10271409 13.37934 7.156077e-03 0.9325867996
## 62 0.00000000 13.60530 0.000000e+00 1.0000000000
## 63 -2.08562113 13.44990 2.513718e+00 0.1129025742
## 64 -2.41848774 13.47900 3.452454e+00 0.0631980623
## 65 -1.31631698 13.44363 1.442953e+00 0.2387063266
## 66 -4.26653955 13.69532 7.984091e+00 0.0047317991
## 67 0.00000000 13.76312 0.000000e+00 1.0000000000
## 68 -0.78853159 13.86628 3.731644e-01 0.5413034164
## 69 -2.59542730 13.40173 4.030988e+00 0.0447084452
## 70 -1.48862475 13.45440 1.229150e+00 0.2676088827
## 71 1.00497694 13.49273 6.137506e-01 0.4334044691
## 72 2.75882625 13.50005 4.255190e+00 0.0391657633
## 73 0.00000000 13.81467 0.000000e+00 1.0000000000
## 74 -1.07930479 13.52852 6.727851e-01 0.4121089950
## 75 -1.40284112 13.51817 1.231402e+00 0.2671710214
## 76 0.00000000 13.37168 0.000000e+00 1.0000000000
## 77 -3.74451540 13.61918 6.734916e+00 0.0094732333
## 78 0.00000000 13.60733 0.000000e+00 1.0000000000
## 79 0.11499957 13.75241 8.263817e-03 0.9275701361
## 80 -1.23745319 13.79298 9.393824e-01 0.3324687347
## 81 -4.03639597 13.40086 8.078142e+00 0.0044926275
## 82 -3.31917929 13.44297 5.778459e+00 0.0162484649
## 83 -2.26614158 14.14651 2.598580e+00 0.1070026247
## 84 -3.29545779 13.66468 5.374707e+00 0.0204581929
## 85 -2.14495397 13.73759 2.374167e+00 0.1234005721
## 86 -1.07825469 13.86357 7.279766e-01 0.3935677605
## 87 -2.77844393 13.52952 4.119874e+00 0.0424183386
## 88 0.00000000 13.50632 0.000000e+00 1.0000000000
## 89 0.00000000 13.51764 0.000000e+00 1.0000000000
## 90 0.00000000 13.54032 0.000000e+00 1.0000000000
## 91 -0.86329262 13.37634 4.761634e-01 0.4901871882
## 92 0.00000000 13.48728 0.000000e+00 1.0000000000
## 93 1.37023164 13.43366 1.210221e+00 0.2713246035
## 94 0.47577986 13.54976 1.510523e-01 0.6975431036
## 95 1.12412212 13.48262 8.179744e-01 0.3658028354
## 96 -4.03913719 13.52548 8.027555e+00 0.0046196980
## 97 -1.86799994 13.59978 2.340097e+00 0.1261249260
## 98 4.33675759 13.35715 9.220761e+00 0.0024012824
## 99 -1.84856974 13.63839 2.262047e+00 0.1326218392
## 100 -1.14029854 13.47232 7.724358e-01 0.3794934127
## 101 4.69290178 13.43810 1.041356e+01 0.0012564392
## 102 -1.15233632 13.57292 8.426612e-01 0.3586670090
## 103 3.56423438 13.56255 6.588759e+00 0.0102821675
## 104 -3.93052221 13.71757 6.989581e+00 0.0082160337
## 105 1.23979514 13.40581 1.373329e+00 0.2412788996
## 106 1.11644111 13.35424 7.815050e-01 0.3767102775
## 107 0.00000000 13.47436 0.000000e+00 1.0000000000
## 108 0.00000000 13.44768 0.000000e+00 1.0000000000
## 109 1.24393376 13.42854 9.940712e-01 0.3187823160
## 110 -1.74061498 13.63154 1.546403e+00 0.2137070806
## 111 0.88203403 13.61379 4.869418e-01 0.4853168412
## 112 1.89277862 13.53310 2.190653e+00 0.1388934736
## 113 -2.21016773 13.56402 2.651577e+00 0.1034902775
## 114 -2.48489839 13.36727 3.656906e+00 0.0558762073
## 115 -2.33895924 13.40091 3.024897e+00 0.0820375496
## 116 0.54211110 13.34520 1.822958e-01 0.6694202121
## 117 0.18065407 13.51755 2.179331e-02 0.8826423306
## 118 1.44282771 13.62102 1.261409e+00 0.2614213803
## 119 -0.86359681 13.57229 4.756465e-01 0.4904227708
## 120 -0.53455138 13.45722 1.618148e-01 0.6875028854
## 121 0.18303420 13.41630 2.144482e-02 0.8835776929
## 122 0.00000000 13.56732 0.000000e+00 1.0000000000
## 123 -2.35606668 13.35999 3.058840e+00 0.0803408894
## 124 0.38898527 13.43956 1.000454e-01 0.7517842324
## 125 -0.14043117 13.58885 1.093063e-02 0.9167360152
## 126 -0.89273853 13.34491 4.860432e-01 0.4857198005
## 127 0.41764644 13.71709 1.055548e-01 0.7452721403
## 128 -0.48398229 13.43133 1.334395e-01 0.7149027621
## 129 -1.81082373 13.51855 1.955411e+00 0.1620472648
## 130 -1.33474139 13.52158 1.089315e+00 0.2966575199
## 131 -1.31837294 13.69632 1.334594e+00 0.2480272764
## 132 1.94749926 13.44207 2.293410e+00 0.1299673636
## 133 3.55252660 13.47284 6.445521e+00 0.0111437756
## 134 -3.27956733 13.40412 5.753309e+00 0.0164824923
## 135 -1.31610156 13.46054 1.420361e+00 0.2387063266
## 136 -2.99509162 13.33935 5.023291e+00 0.0250384492
## 137 -3.02843647 13.50793 4.979464e+00 0.0256800896
## 138 0.00000000 13.66936 0.000000e+00 1.0000000000
## 139 0.56110295 13.51027 2.084137e-01 0.6480271386
## 140 0.42572842 13.45104 1.201445e-01 0.7288878198
## 141 0.00000000 13.90230 0.000000e+00 1.0000000000
## 142 -0.31654057 13.44995 6.703881e-02 0.7957053668
## 143 -1.46460464 13.44891 1.271881e+00 0.2594510374
## 144 0.00000000 13.69839 0.000000e+00 1.0000000000
## 145 0.00000000 13.45455 0.000000e+00 1.0000000000
## 146 -0.45889467 13.34604 1.221405e-01 0.7267345380
## 147 -0.34764580 13.76154 6.764604e-02 0.7948028036
## 148 -4.44237893 13.70972 8.588436e+00 0.0033935021
## 149 1.29043991 13.35677 1.014851e+00 0.3137767370
## 150 -1.08632618 13.40062 7.085753e-01 0.3999446988
## 151 -3.13720040 13.84061 5.238422e+00 0.0221216622
## 152 -1.07276972 13.56229 7.141939e-01 0.3980826609
## 153 0.00000000 13.49824 0.000000e+00 1.0000000000
## 154 -1.93799822 13.65321 2.356573e+00 0.1247992388
## 155 -0.70284723 13.68759 2.930217e-01 0.5883071019
## 156 -0.12690187 13.67610 9.483688e-03 0.9224239331
## 157 -4.08219672 13.54271 8.250414e+00 0.0040859793
## 158 -3.84847407 13.61731 7.020662e+00 0.0080747600
## 159 -3.18229259 13.51256 5.270809e+00 0.0217140598
## 160 -2.01537270 13.36558 2.644418e+00 0.1039572843
## 161 -0.69603827 13.84341 3.017281e-01 0.5828178487
## 162 -1.24581570 13.86275 8.467323e-01 0.3575087190
## 163 3.31226977 13.41472 5.752705e+00 0.0164881563
## 164 -1.50052682 13.40263 1.285880e+00 0.2568457024
## 165 0.92805563 13.35591 5.414693e-01 0.4618480113
## 166 3.32500206 13.45104 5.846819e+00 0.0156294863
## 167 -2.80229893 13.59922 4.249893e+00 0.0392880415
## 168 -0.64636149 13.41221 2.668902e-01 0.6054411249
## 169 -1.61746768 13.40073 1.569474e+00 0.2103234386
## 170 -4.35116708 13.85574 8.789711e+00 0.0030391116
## 171 0.13043721 13.72894 4.511753e-03 0.9464485335
## 172 -2.99988075 13.57200 4.923828e+00 0.0265193144
## 173 0.53036761 13.65042 1.690566e-01 0.6809636743
## 174 1.19918272 13.77843 1.297415e+00 0.2547231745
## 175 -1.41776318 13.44345 1.144274e+00 0.2847862832
## 176 -0.71525218 13.75587 2.629746e-01 0.6080993973
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## 183 -3.41934306 13.54679 6.094176e+00 0.0135854904
## 184 1.45002063 13.47427 1.258415e+00 0.2619882122
## 185 3.35985954 13.45657 5.877929e+00 0.0153559032
## 186 2.62607945 13.62717 3.706016e+00 0.0542553613
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## 195 -1.23069068 13.37612 1.370712e+00 0.2417277227
## 196 -3.88690103 13.41811 7.582547e+00 0.0059081539
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## 198 -0.84726480 13.39441 4.603451e-01 0.4974841771
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## 200 -0.63760813 13.63085 2.338119e-01 0.6287260829
## 201 -3.01866022 13.42843 5.050635e+00 0.0246465740
## 202 1.59492277 13.55673 1.619270e+00 0.2032340829
## 203 -1.04289285 13.55092 6.228773e-01 0.4300056455
## 204 -2.48391968 13.50278 3.581366e+00 0.0584705193
## 205 1.02496778 13.55959 6.770373e-01 0.4106355889
## 206 -2.91005184 13.65624 4.416868e+00 0.0356193934
## 207 -3.36777312 13.65008 5.288565e+00 0.0214939042
## 208 -0.52522390 13.41700 1.543979e-01 0.6943789163
## 209 1.19753396 13.95992 1.272218e+00 0.2593878772
## 210 -0.31119964 13.46826 6.165292e-02 0.8039092163
## 211 -2.02672673 13.91102 2.612817e+00 0.1060463785
## 212 0.00000000 13.52755 0.000000e+00 1.0000000000
## 213 -2.96918613 13.51234 4.844690e+00 0.0277624728
## 214 -0.45102549 13.56899 1.349716e-01 0.7133425905
## 215 -1.26298922 13.53953 1.018441e+00 0.3129224078
## 216 1.67464088 13.50192 1.728205e+00 0.1886814275
## 217 1.02738722 13.73670 6.267990e-01 0.4285575619
## 218 3.32322396 13.46521 5.667858e+00 0.0173039763
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## 222 1.78970653 13.50459 1.895900e+00 0.1685800248
## 223 -0.40753920 13.59740 1.025575e-01 0.7487910112
## 224 -0.36552299 13.80770 8.028482e-02 0.7769198177
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## 227 -2.63269284 13.39826 4.105298e+00 0.0427852402
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## 230 -0.16040021 13.43667 1.543215e-02 0.9973410612
## 231 -0.43874053 13.66098 1.155685e-01 0.7339011375
## 232 -0.47958098 13.51337 1.343587e-01 0.7139655556
## 233 1.07723482 13.87744 7.115414e-01 0.3989601298
## 234 0.00000000 13.45905 0.000000e+00 1.0000000000
## 235 -1.06738783 13.32179 7.055456e-01 0.4009539803
## 236 0.33606850 13.50059 6.769650e-02 0.7947279933
## 237 -1.20034505 13.43528 8.901929e-01 0.3454561771
## 238 0.00000000 13.35589 0.000000e+00 1.0000000000
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## 240 0.00000000 13.59416 0.000000e+00 1.0000000000
## 241 2.05636533 13.40591 2.438816e+00 0.1184087562
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## 243 -2.48595030 13.61199 3.458627e+00 0.0629626136
## 244 0.17636914 14.18502 1.440074e-02 0.9044840102
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## 251 -1.61161610 13.81281 1.337521e+00 0.2475094293
## 252 -1.27650766 13.64208 9.255335e-01 0.3360580106
## 253 2.34077072 13.51906 3.128768e+00 0.0769635029
## 254 -1.18691277 13.58071 7.576713e-01 0.3840867967
## 255 -1.31547243 13.52878 1.402425e+00 0.2387063266
## 256 -2.03160249 13.76500 2.210253e+00 0.1371392138
## 257 -1.91892380 13.46499 2.013599e+00 0.1559376606
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## 259 0.57122391 13.82549 2.038001e-01 0.6516841777
## 260 -2.47846212 13.41564 3.633955e+00 0.0566512431
## 261 -1.32491255 13.56078 1.425378e+00 0.2387063272
## 262 0.00000000 13.64891 0.000000e+00 1.0000000000
## 263 -3.15898346 13.74338 4.979407e+00 0.0256809397
## 264 4.89450095 13.49119 1.096297e+01 0.0009340067
## 265 -1.83477198 13.47796 2.344059e+00 0.1258046843
## 266 0.37854581 13.44549 8.543983e-02 0.7700648305
## 267 0.00000000 13.45964 0.000000e+00 1.0000000000
## 268 -1.85299098 13.54191 2.392544e+00 0.1219583356
## 269 -3.71317385 13.39058 7.046395e+00 0.0079596767
## 270 -3.01863524 13.54937 5.014779e+00 0.0251617532
## 271 -4.44690342 13.73699 8.721726e+00 0.0031543984
## 272 0.00000000 13.56137 0.000000e+00 1.0000000000
## 273 0.33628287 13.54648 7.386655e-02 0.7857957571
## 274 -2.30893573 13.67065 2.591576e+00 0.1074764853
## 275 -0.68293006 13.90515 2.909616e-01 0.5896214022
## 276 -1.31640429 13.39260 1.437970e+00 0.2387063266
## 277 -2.04684846 13.59869 2.308495e+00 0.1287117527
## 278 -1.20851732 13.43400 1.357389e+00 0.2440284839
## 279 -0.74808506 13.65479 3.237739e-01 0.5693658859
## 280 -0.40405745 13.45414 9.572109e-02 0.7570350121
## 281 -2.97404296 13.57492 4.855191e+00 0.0275940954
## 282 -0.88076829 13.44054 4.905595e-01 0.4837001033
## 283 -2.27160146 13.62433 3.089619e+00 0.0788350647
## 284 4.53918890 13.40226 9.871298e+00 0.0016854662
## 285 -1.20931300 13.68511 7.949361e-01 0.3726410302
## 286 -2.77881723 13.47030 4.311978e+00 0.0378797386
## 287 -3.29241475 13.45748 5.666705e+00 0.0173153442
## 288 -0.91586019 13.48179 5.279196e-01 0.4675060542
## 289 0.00000000 13.61105 0.000000e+00 1.0000000000
## 290 -0.78307069 13.46150 3.599077e-01 0.5485760509
## 291 -1.86851353 13.40060 2.443502e+00 0.1180557523
## 292 2.45624852 13.43164 3.420051e+00 0.0644493011
## 293 0.58017423 13.64982 1.947146e-01 0.6590343481
## 294 0.48919152 13.76433 1.487775e-01 0.6997176131
## 295 2.60908540 13.48565 3.780661e+00 0.0518864394
## 296 -4.24694318 13.59824 8.441698e+00 0.0036781233
## 297 2.51614846 13.48484 3.567033e+00 0.0589770250
## 298 -3.06781257 13.47165 5.055532e+00 0.0245770666
## 299 1.42972350 13.45967 1.265599e+00 0.2606307412
## 300 -1.20540842 13.70740 1.250569e+00 0.2634805331
## 301 0.02789964 13.50960 2.862390e-04 0.9865020155
## 302 0.05057833 13.59096 1.002290e-03 0.9747448835
## 303 -1.86961025 13.49716 2.396328e+00 0.1216636414
## 304 -2.00783208 13.42699 2.634343e+00 0.1046183723
## 305 -3.23536805 13.42448 5.651341e+00 0.0174675738
## 306 -2.78484474 13.39131 4.406777e+00 0.0358305705
## 307 -0.68657392 13.42233 3.077238e-01 0.5790972428
## 308 0.00000000 13.37060 0.000000e+00 1.0000000000
## 309 -0.81474010 13.73940 3.969180e-01 0.5287049263
## 310 -2.30539877 13.68493 2.769794e+00 0.0961013186
## 311 -1.33400833 13.38529 1.452213e+00 0.2387063277
## 312 0.00000000 13.80527 0.000000e+00 1.0000000000
## 313 -1.20671252 13.62962 1.273054e+00 0.2592314951
## 314 1.28683892 13.41150 1.036817e+00 0.3085965215
## 315 -0.66583341 13.49524 2.487583e-01 0.6179657320
## 316 -4.65615067 13.66151 9.311926e+00 0.0022848286
## 317 -1.28116064 13.41983 9.676393e-01 0.3253021431
## 318 -1.95287092 13.43198 2.562649e+00 0.1094582567
## 319 0.04167786 13.55164 1.412587e-03 0.9700200727
## 320 -3.57602780 13.57799 6.540129e+00 0.0105667494
## 321 1.08904932 13.35989 6.770181e-01 0.4106422400
## 322 -1.22618006 14.23674 1.023854e+00 0.3116400508
## 323 -1.55153451 13.50569 1.433399e+00 0.2312492234
## 324 3.14483888 13.62761 4.968409e+00 0.0258446175
## 325 0.22407834 13.62782 3.062743e-02 0.8610790285
## 326 -1.31575059 13.49132 1.403801e+00 0.2387063266
## 327 0.43680985 13.37126 1.243029e-01 0.7244238134
## 328 3.17539493 13.43696 5.308495e+00 0.0212495571
## 329 -0.16053553 13.43114 1.699955e-02 0.8962675296
## 330 -1.00486503 13.55273 6.526873e-01 0.4191797755
## 331 -4.60895948 13.45477 1.006182e+01 0.0015199879
## 332 -3.22186380 13.76578 5.017936e+00 0.0251159423
## 333 -4.53450331 13.86203 9.408191e+00 0.0021680700
## 334 0.00000000 13.34440 0.000000e+00 1.0000000000
## 335 -3.85810003 13.31546 7.664119e+00 0.0056471447
## 336 4.85734299 13.49811 1.082209e+01 0.0010077043
## 337 1.68893110 13.44329 1.795121e+00 0.1803450124
## 338 -0.69276032 13.37195 2.882772e-01 0.5913430066
## 339 0.00000000 13.69677 0.000000e+00 1.0000000000
## 340 -0.02501548 13.50882 3.953812e-04 0.9969297217
## 341 0.00000000 13.45008 0.000000e+00 1.0000000000
## 342 0.00000000 13.60730 0.000000e+00 1.0000000000
## 343 -0.55445052 13.44730 1.902547e-01 0.6627176203
## 344 -0.39768003 13.56373 9.229381e-02 0.7612896937
## 345 -2.66533027 13.41537 4.160402e+00 0.0414154176
## 346 -1.53135419 13.43140 1.405177e+00 0.2358971382
## 347 0.04777135 13.60026 1.264767e-03 0.9716313323
## 348 0.00000000 13.42919 0.000000e+00 1.0000000000
## 349 -1.14501930 13.56201 8.181277e-01 0.3657579124
## 350 -1.38791913 13.62033 1.120269e+00 0.2898954730
## 351 -2.72282957 13.45709 4.259408e+00 0.0390686948
## 352 -0.80832073 13.59047 4.065417e-01 0.5237499587
## 353 4.20578610 13.33058 8.812723e+00 0.0030010651
## 354 -0.73957639 13.33649 3.467680e-01 0.5559665608
## 355 -1.69864614 13.78526 1.658282e+00 0.1978761588
## 356 -0.51750240 13.58902 1.615312e-01 0.6877624448
## 357 -2.69003811 13.55936 3.885642e+00 0.0487382350
## 358 2.92737300 13.39231 4.595203e+00 0.0320943899
## 359 0.00000000 13.56163 0.000000e+00 1.0000000000
## 360 2.93998866 13.36697 4.576997e+00 0.0324369260
## 361 -0.33742206 13.45854 6.845257e-02 0.7936106721
## 362 -1.64541862 13.43326 1.602580e+00 0.2055781901
## 363 3.70461051 13.58793 6.771909e+00 0.0092790325
## 364 -1.08487452 13.44170 6.884867e-01 0.4067066355
## 365 -1.27136857 13.49282 9.836410e-01 0.3213343320
## 366 -2.13330917 13.55085 2.522447e+00 0.1122794624
## FDR Nhood SpatialFDR contrast
## 1 0.71908663 1 0.73606580 Age1wk - Age4wk
## 2 0.31164288 2 0.30949800 Age1wk - Age4wk
## 3 0.98357111 3 0.99454290 Age1wk - Age4wk
## 4 0.38015443 4 0.37624693 Age1wk - Age4wk
## 5 0.24103282 5 0.24095128 Age1wk - Age4wk
## 6 0.57071727 6 0.58315112 Age1wk - Age4wk
## 7 0.70048453 7 0.71842809 Age1wk - Age4wk
## 8 0.38139918 8 0.37766393 Age1wk - Age4wk
## 9 1.00000000 9 1.00000000 Age1wk - Age4wk
## 10 0.09114939 10 0.10045006 Age1wk - Age4wk
## 11 0.56725809 11 0.58077260 Age1wk - Age4wk
## 12 0.63100157 12 0.64312065 Age1wk - Age4wk
## 13 0.56725809 13 0.58077260 Age1wk - Age4wk
## 14 0.72228713 14 0.73606580 Age1wk - Age4wk
## 15 1.00000000 15 1.00000000 Age1wk - Age4wk
## 16 1.00000000 16 1.00000000 Age1wk - Age4wk
## 17 1.00000000 17 1.00000000 Age1wk - Age4wk
## 18 0.56725809 18 0.57227860 Age1wk - Age4wk
## 19 0.64823731 19 0.65862315 Age1wk - Age4wk
## 20 0.31066707 20 0.30949800 Age1wk - Age4wk
## 21 0.44764617 21 0.45690049 Age1wk - Age4wk
## 22 0.27113154 22 0.27283998 Age1wk - Age4wk
## 23 0.70552479 23 0.72585904 Age1wk - Age4wk
## 24 0.36762985 24 0.36523002 Age1wk - Age4wk
## 25 0.23471308 25 0.23383778 Age1wk - Age4wk
## 26 0.11549840 26 0.12101680 Age1wk - Age4wk
## 27 1.00000000 27 1.00000000 Age1wk - Age4wk
## 28 1.00000000 28 1.00000000 Age1wk - Age4wk
## 29 0.92416311 29 0.92233488 Age1wk - Age4wk
## 30 0.86468014 30 0.86756775 Age1wk - Age4wk
## 31 0.69593162 31 0.71128448 Age1wk - Age4wk
## 32 0.63409961 32 0.64312065 Age1wk - Age4wk
## 33 0.99395278 33 1.00000000 Age1wk - Age4wk
## 34 0.98357111 34 0.99503656 Age1wk - Age4wk
## 35 0.99395278 35 1.00000000 Age1wk - Age4wk
## 36 0.56725809 36 0.57491903 Age1wk - Age4wk
## 37 1.00000000 37 1.00000000 Age1wk - Age4wk
## 38 0.16594965 38 0.17200603 Age1wk - Age4wk
## 39 0.68268980 39 0.69494957 Age1wk - Age4wk
## 40 0.38015443 40 0.37624693 Age1wk - Age4wk
## 41 0.97015675 41 0.97773294 Age1wk - Age4wk
## 42 1.00000000 42 1.00000000 Age1wk - Age4wk
## 43 0.92416311 43 0.92233488 Age1wk - Age4wk
## 44 0.46310785 44 0.47528615 Age1wk - Age4wk
## 45 1.00000000 45 1.00000000 Age1wk - Age4wk
## 46 0.35746153 46 0.35826618 Age1wk - Age4wk
## 47 0.16594965 47 0.17200603 Age1wk - Age4wk
## 48 1.00000000 48 1.00000000 Age1wk - Age4wk
## 49 0.89902849 49 0.90366144 Age1wk - Age4wk
## 50 1.00000000 50 1.00000000 Age1wk - Age4wk
## 51 0.29230206 51 0.29360199 Age1wk - Age4wk
## 52 0.31066707 52 0.30856475 Age1wk - Age4wk
## 53 0.35104736 53 0.35036492 Age1wk - Age4wk
## 54 0.90623965 54 0.90436924 Age1wk - Age4wk
## 55 1.00000000 55 1.00000000 Age1wk - Age4wk
## 56 0.31276816 56 0.31045281 Age1wk - Age4wk
## 57 0.71908663 57 0.73606580 Age1wk - Age4wk
## 58 0.81851967 58 0.81965873 Age1wk - Age4wk
## 59 1.00000000 59 1.00000000 Age1wk - Age4wk
## 60 0.72228713 60 0.73606580 Age1wk - Age4wk
## 61 1.00000000 61 1.00000000 Age1wk - Age4wk
## 62 1.00000000 62 1.00000000 Age1wk - Age4wk
## 63 0.37565766 63 0.37131440 Age1wk - Age4wk
## 64 0.27113154 64 0.27283998 Age1wk - Age4wk
## 65 0.56725809 65 0.57227860 Age1wk - Age4wk
## 66 0.09114939 66 0.10045006 Age1wk - Age4wk
## 67 1.00000000 67 1.00000000 Age1wk - Age4wk
## 68 0.83947903 68 0.84553872 Age1wk - Age4wk
## 69 0.22112555 69 0.22013974 Age1wk - Age4wk
## 70 0.56944681 70 0.58185549 Age1wk - Age4wk
## 71 0.72228713 71 0.73606580 Age1wk - Age4wk
## 72 0.20839744 72 0.20893591 Age1wk - Age4wk
## 73 1.00000000 73 1.00000000 Age1wk - Age4wk
## 74 0.71147119 74 0.72776145 Age1wk - Age4wk
## 75 0.56944681 75 0.58185549 Age1wk - Age4wk
## 76 1.00000000 76 1.00000000 Age1wk - Age4wk
## 77 0.11955874 77 0.12999020 Age1wk - Age4wk
## 78 1.00000000 78 1.00000000 Age1wk - Age4wk
## 79 1.00000000 79 1.00000000 Age1wk - Age4wk
## 80 0.64823731 80 0.65862315 Age1wk - Age4wk
## 81 0.09114939 81 0.10045006 Age1wk - Age4wk
## 82 0.15221743 82 0.16460008 Age1wk - Age4wk
## 83 0.36762985 83 0.36523002 Age1wk - Age4wk
## 84 0.16594965 84 0.17200603 Age1wk - Age4wk
## 85 0.38150184 85 0.38136289 Age1wk - Age4wk
## 86 0.70552479 86 0.72585904 Age1wk - Age4wk
## 87 0.21451230 87 0.21443720 Age1wk - Age4wk
## 88 1.00000000 88 1.00000000 Age1wk - Age4wk
## 89 1.00000000 89 1.00000000 Age1wk - Age4wk
## 90 1.00000000 90 1.00000000 Age1wk - Age4wk
## 91 0.78381980 91 0.79266407 Age1wk - Age4wk
## 92 1.00000000 92 1.00000000 Age1wk - Age4wk
## 93 0.57071727 93 0.58315112 Age1wk - Age4wk
## 94 0.95203214 94 0.95709869 Age1wk - Age4wk
## 95 0.68658378 95 0.70109158 Age1wk - Age4wk
## 96 0.09114939 96 0.10045006 Age1wk - Age4wk
## 97 0.38150184 97 0.38143543 Age1wk - Age4wk
## 98 0.09114939 98 0.10045006 Age1wk - Age4wk
## 99 0.38831675 99 0.39283690 Age1wk - Age4wk
## 100 0.69796276 100 0.71499691 Age1wk - Age4wk
## 101 0.09114939 101 0.09375152 Age1wk - Age4wk
## 102 0.68268980 102 0.69494957 Age1wk - Age4wk
## 103 0.12359460 103 0.13846980 Age1wk - Age4wk
## 104 0.11549840 104 0.12101680 Age1wk - Age4wk
## 105 0.56725809 105 0.57227860 Age1wk - Age4wk
## 106 0.69634324 106 0.71250721 Age1wk - Age4wk
## 107 1.00000000 107 1.00000000 Age1wk - Age4wk
## 108 1.00000000 108 1.00000000 Age1wk - Age4wk
## 109 0.63409961 109 0.64312065 Age1wk - Age4wk
## 110 0.55869137 110 0.57227860 Age1wk - Age4wk
## 111 0.78314294 111 0.79100271 Age1wk - Age4wk
## 112 0.40027568 112 0.40715956 Age1wk - Age4wk
## 113 0.36762985 113 0.36523002 Age1wk - Age4wk
## 114 0.25563365 114 0.25654278 Age1wk - Age4wk
## 115 0.31276816 115 0.31045281 Age1wk - Age4wk
## 116 0.93158858 116 0.93235877 Age1wk - Age4wk
## 117 1.00000000 117 1.00000000 Age1wk - Age4wk
## 118 0.56725809 118 0.58077260 Age1wk - Age4wk
## 119 0.78381980 119 0.79266407 Age1wk - Age4wk
## 120 0.94631975 120 0.95000490 Age1wk - Age4wk
## 121 1.00000000 121 1.00000000 Age1wk - Age4wk
## 122 1.00000000 122 1.00000000 Age1wk - Age4wk
## 123 0.31276816 123 0.31024932 Age1wk - Age4wk
## 124 0.98268939 124 0.99223946 Age1wk - Age4wk
## 125 1.00000000 125 1.00000000 Age1wk - Age4wk
## 126 0.78314294 126 0.79100271 Age1wk - Age4wk
## 127 0.98118562 127 0.99046770 Age1wk - Age4wk
## 128 0.96196475 128 0.96913640 Age1wk - Age4wk
## 129 0.45622538 129 0.46596150 Age1wk - Age4wk
## 130 0.61342741 130 0.62653297 Age1wk - Age4wk
## 131 0.56725809 131 0.57575383 Age1wk - Age4wk
## 132 0.38526844 132 0.38890436 Age1wk - Age4wk
## 133 0.12359460 133 0.13987381 Age1wk - Age4wk
## 134 0.15221743 134 0.16460008 Age1wk - Age4wk
## 135 0.56725809 135 0.57227860 Age1wk - Age4wk
## 136 0.16594965 136 0.17200603 Age1wk - Age4wk
## 137 0.16594965 137 0.17200603 Age1wk - Age4wk
## 138 1.00000000 138 1.00000000 Age1wk - Age4wk
## 139 0.92416311 139 0.92007578 Age1wk - Age4wk
## 140 0.97008343 140 0.97435595 Age1wk - Age4wk
## 141 1.00000000 141 1.00000000 Age1wk - Age4wk
## 142 0.99395278 142 1.00000000 Age1wk - Age4wk
## 143 0.56725809 143 0.58077260 Age1wk - Age4wk
## 144 1.00000000 144 1.00000000 Age1wk - Age4wk
## 145 1.00000000 145 1.00000000 Age1wk - Age4wk
## 146 0.97008343 146 0.97435595 Age1wk - Age4wk
## 147 0.99395278 147 1.00000000 Age1wk - Age4wk
## 148 0.09114939 148 0.10045006 Age1wk - Age4wk
## 149 0.63100157 149 0.64312065 Age1wk - Age4wk
## 150 0.70552479 150 0.72585904 Age1wk - Age4wk
## 151 0.16594965 151 0.17200603 Age1wk - Age4wk
## 152 0.70552479 152 0.72585904 Age1wk - Age4wk
## 153 1.00000000 153 1.00000000 Age1wk - Age4wk
## 154 0.38150184 154 0.38143543 Age1wk - Age4wk
## 155 0.87980301 155 0.88256211 Age1wk - Age4wk
## 156 1.00000000 156 1.00000000 Age1wk - Age4wk
## 157 0.09114939 157 0.10045006 Age1wk - Age4wk
## 158 0.11549840 158 0.12101680 Age1wk - Age4wk
## 159 0.16594965 159 0.17200603 Age1wk - Age4wk
## 160 0.36762985 160 0.36523002 Age1wk - Age4wk
## 161 0.87782441 161 0.88093908 Age1wk - Age4wk
## 162 0.68268980 162 0.69494957 Age1wk - Age4wk
## 163 0.15221743 163 0.16460008 Age1wk - Age4wk
## 164 0.56725809 164 0.58077260 Age1wk - Age4wk
## 165 0.75801064 165 0.76743784 Age1wk - Age4wk
## 166 0.15221743 166 0.16460008 Age1wk - Age4wk
## 167 0.20839744 167 0.20893591 Age1wk - Age4wk
## 168 0.89713138 168 0.89871130 Age1wk - Age4wk
## 169 0.55380128 169 0.57143469 Age1wk - Age4wk
## 170 0.09114939 170 0.10045006 Age1wk - Age4wk
## 171 1.00000000 171 1.00000000 Age1wk - Age4wk
## 172 0.16657484 172 0.17200603 Age1wk - Age4wk
## 173 0.94406328 173 0.94597913 Age1wk - Age4wk
## 174 0.56725809 174 0.58077260 Age1wk - Age4wk
## 175 0.59561017 175 0.60614481 Age1wk - Age4wk
## 176 0.89743701 176 0.90124072 Age1wk - Age4wk
## 177 1.00000000 177 1.00000000 Age1wk - Age4wk
## 178 0.90623965 178 0.90436924 Age1wk - Age4wk
## 179 1.00000000 179 1.00000000 Age1wk - Age4wk
## 180 0.92416311 180 0.92233488 Age1wk - Age4wk
## 181 1.00000000 181 1.00000000 Age1wk - Age4wk
## 182 0.69938193 182 0.71634713 Age1wk - Age4wk
## 183 0.14624381 183 0.16414179 Age1wk - Age4wk
## 184 0.56725809 184 0.58077260 Age1wk - Age4wk
## 185 0.15221743 185 0.16460008 Age1wk - Age4wk
## 186 0.25136028 186 0.25291250 Age1wk - Age4wk
## 187 0.56725809 187 0.57227860 Age1wk - Age4wk
## 188 0.11549840 188 0.12101680 Age1wk - Age4wk
## 189 0.92416311 189 0.91910842 Age1wk - Age4wk
## 190 0.11549840 190 0.12247835 Age1wk - Age4wk
## 191 1.00000000 191 1.00000000 Age1wk - Age4wk
## 192 0.09114939 192 0.09375152 Age1wk - Age4wk
## 193 0.38526844 193 0.38902902 Age1wk - Age4wk
## 194 0.74020447 194 0.75560835 Age1wk - Age4wk
## 195 0.56725809 195 0.57227860 Age1wk - Age4wk
## 196 0.10297068 196 0.10765200 Age1wk - Age4wk
## 197 0.75801064 197 0.76743784 Age1wk - Age4wk
## 198 0.79164873 198 0.80028649 Age1wk - Age4wk
## 199 1.00000000 199 1.00000000 Age1wk - Age4wk
## 200 0.90954050 200 0.90901274 Age1wk - Age4wk
## 201 0.16594965 201 0.17200603 Age1wk - Age4wk
## 202 0.54294653 202 0.56047672 Age1wk - Age4wk
## 203 0.72228713 203 0.73606580 Age1wk - Age4wk
## 204 0.26006736 204 0.26017165 Age1wk - Age4wk
## 205 0.71147119 205 0.72776145 Age1wk - Age4wk
## 206 0.20175367 206 0.20411658 Age1wk - Age4wk
## 207 0.16594965 207 0.17200603 Age1wk - Age4wk
## 208 0.95184526 208 0.95570524 Age1wk - Age4wk
## 209 0.56725809 209 0.58077260 Age1wk - Age4wk
## 210 1.00000000 210 1.00000000 Age1wk - Age4wk
## 211 0.36762985 211 0.36523002 Age1wk - Age4wk
## 212 1.00000000 212 1.00000000 Age1wk - Age4wk
## 213 0.16657484 213 0.17200603 Age1wk - Age4wk
## 214 0.96196475 214 0.96913640 Age1wk - Age4wk
## 215 0.63100157 215 0.64312065 Age1wk - Age4wk
## 216 0.51153631 216 0.52578743 Age1wk - Age4wk
## 217 0.72228713 217 0.73606580 Age1wk - Age4wk
## 218 0.15221743 218 0.16460008 Age1wk - Age4wk
## 219 0.83311788 219 0.83757160 Age1wk - Age4wk
## 220 0.83394268 220 0.83782566 Age1wk - Age4wk
## 221 0.21349356 221 0.21425166 Age1wk - Age4wk
## 222 0.46742643 222 0.47948987 Age1wk - Age4wk
## 223 0.98228498 223 0.99223946 Age1wk - Age4wk
## 224 0.99395278 224 1.00000000 Age1wk - Age4wk
## 225 0.56725809 225 0.57227860 Age1wk - Age4wk
## 226 1.00000000 226 1.00000000 Age1wk - Age4wk
## 227 0.21451230 227 0.21443720 Age1wk - Age4wk
## 228 1.00000000 228 1.00000000 Age1wk - Age4wk
## 229 0.12359460 229 0.13985179 Age1wk - Age4wk
## 230 1.00000000 230 1.00000000 Age1wk - Age4wk
## 231 0.97015675 231 0.97773294 Age1wk - Age4wk
## 232 0.96196475 232 0.96913640 Age1wk - Age4wk
## 233 0.70552479 233 0.72585904 Age1wk - Age4wk
## 234 1.00000000 234 1.00000000 Age1wk - Age4wk
## 235 0.70552479 235 0.72585904 Age1wk - Age4wk
## 236 0.99395278 236 1.00000000 Age1wk - Age4wk
## 237 0.66545769 237 0.67605524 Age1wk - Age4wk
## 238 1.00000000 238 1.00000000 Age1wk - Age4wk
## 239 0.56725809 239 0.57227860 Age1wk - Age4wk
## 240 1.00000000 240 1.00000000 Age1wk - Age4wk
## 241 0.38015443 241 0.37624693 Age1wk - Age4wk
## 242 1.00000000 242 1.00000000 Age1wk - Age4wk
## 243 0.27113154 243 0.27283998 Age1wk - Age4wk
## 244 1.00000000 244 1.00000000 Age1wk - Age4wk
## 245 1.00000000 245 1.00000000 Age1wk - Age4wk
## 246 0.48129123 246 0.49354784 Age1wk - Age4wk
## 247 1.00000000 247 1.00000000 Age1wk - Age4wk
## 248 0.92416311 248 0.91910842 Age1wk - Age4wk
## 249 0.16657484 249 0.17200603 Age1wk - Age4wk
## 250 0.35746153 250 0.35826618 Age1wk - Age4wk
## 251 0.56725809 251 0.57575383 Age1wk - Age4wk
## 252 0.65077900 252 0.66200231 Age1wk - Age4wk
## 253 0.31066707 253 0.30949800 Age1wk - Age4wk
## 254 0.69938193 254 0.71634713 Age1wk - Age4wk
## 255 0.56725809 255 0.57227860 Age1wk - Age4wk
## 256 0.39835676 256 0.40425253 Age1wk - Age4wk
## 257 0.44588425 257 0.45329772 Age1wk - Age4wk
## 258 0.85370086 258 0.85440395 Age1wk - Age4wk
## 259 0.92416311 259 0.92233488 Age1wk - Age4wk
## 260 0.25597969 260 0.25664782 Age1wk - Age4wk
## 261 0.56725809 261 0.57227860 Age1wk - Age4wk
## 262 1.00000000 262 1.00000000 Age1wk - Age4wk
## 263 0.16594965 263 0.17200603 Age1wk - Age4wk
## 264 0.09114939 264 0.09375152 Age1wk - Age4wk
## 265 0.38150184 265 0.38143543 Age1wk - Age4wk
## 266 0.98892536 266 0.99876360 Age1wk - Age4wk
## 267 1.00000000 267 1.00000000 Age1wk - Age4wk
## 268 0.38150184 268 0.37859013 Age1wk - Age4wk
## 269 0.11549840 269 0.12101680 Age1wk - Age4wk
## 270 0.16594965 270 0.17200603 Age1wk - Age4wk
## 271 0.09114939 271 0.10045006 Age1wk - Age4wk
## 272 1.00000000 272 1.00000000 Age1wk - Age4wk
## 273 0.99395278 273 1.00000000 Age1wk - Age4wk
## 274 0.36762985 274 0.36523002 Age1wk - Age4wk
## 275 0.87980301 275 0.88256211 Age1wk - Age4wk
## 276 0.56725809 276 0.57227860 Age1wk - Age4wk
## 277 0.38526844 277 0.38716991 Age1wk - Age4wk
## 278 0.56725809 278 0.57227860 Age1wk - Age4wk
## 279 0.86468014 279 0.86756775 Age1wk - Age4wk
## 280 0.98357111 280 0.99454290 Age1wk - Age4wk
## 281 0.16657484 281 0.17200603 Age1wk - Age4wk
## 282 0.78314294 282 0.79100271 Age1wk - Age4wk
## 283 0.31164288 283 0.30949800 Age1wk - Age4wk
## 284 0.09114939 284 0.09375152 Age1wk - Age4wk
## 285 0.69585009 285 0.71128448 Age1wk - Age4wk
## 286 0.20839744 286 0.20893591 Age1wk - Age4wk
## 287 0.15221743 287 0.16460008 Age1wk - Age4wk
## 288 0.76387150 288 0.77300676 Age1wk - Age4wk
## 289 1.00000000 289 1.00000000 Age1wk - Age4wk
## 290 0.84716808 290 0.85292331 Age1wk - Age4wk
## 291 0.38015443 291 0.37624693 Age1wk - Age4wk
## 292 0.27113154 292 0.27283998 Age1wk - Age4wk
## 293 0.92416311 293 0.92375449 Age1wk - Age4wk
## 294 0.95203214 294 0.95844726 Age1wk - Age4wk
## 295 0.24346714 295 0.24321808 Age1wk - Age4wk
## 296 0.09114939 296 0.10045006 Age1wk - Age4wk
## 297 0.26006736 297 0.26057792 Age1wk - Age4wk
## 298 0.16594965 298 0.17200603 Age1wk - Age4wk
## 299 0.56725809 299 0.58077260 Age1wk - Age4wk
## 300 0.56725809 300 0.58077260 Age1wk - Age4wk
## 301 1.00000000 301 1.00000000 Age1wk - Age4wk
## 302 1.00000000 302 1.00000000 Age1wk - Age4wk
## 303 0.38150184 303 0.37859013 Age1wk - Age4wk
## 304 0.36762985 304 0.36523002 Age1wk - Age4wk
## 305 0.15221743 305 0.16460008 Age1wk - Age4wk
## 306 0.20175367 306 0.20411658 Age1wk - Age4wk
## 307 0.87582476 307 0.87729377 Age1wk - Age4wk
## 308 1.00000000 308 1.00000000 Age1wk - Age4wk
## 309 0.83049787 309 0.83502193 Age1wk - Age4wk
## 310 0.35746153 310 0.35826618 Age1wk - Age4wk
## 311 0.56725809 311 0.57227860 Age1wk - Age4wk
## 312 1.00000000 312 1.00000000 Age1wk - Age4wk
## 313 0.56725809 313 0.58077260 Age1wk - Age4wk
## 314 0.63100157 314 0.64312065 Age1wk - Age4wk
## 315 0.90470183 315 0.90436924 Age1wk - Age4wk
## 316 0.09114939 316 0.10045006 Age1wk - Age4wk
## 317 0.64011067 317 0.64719669 Age1wk - Age4wk
## 318 0.37094187 318 0.36523002 Age1wk - Age4wk
## 319 1.00000000 319 1.00000000 Age1wk - Age4wk
## 320 0.12359460 320 0.13873674 Age1wk - Age4wk
## 321 0.71147119 321 0.72776145 Age1wk - Age4wk
## 322 0.63100157 322 0.64312065 Age1wk - Age4wk
## 323 0.56725809 323 0.57227860 Age1wk - Age4wk
## 324 0.16594965 324 0.17200603 Age1wk - Age4wk
## 325 1.00000000 325 1.00000000 Age1wk - Age4wk
## 326 0.56725809 326 0.57227860 Age1wk - Age4wk
## 327 0.97008343 327 0.97435595 Age1wk - Age4wk
## 328 0.16594965 328 0.17200603 Age1wk - Age4wk
## 329 1.00000000 329 1.00000000 Age1wk - Age4wk
## 330 0.71908663 330 0.73606580 Age1wk - Age4wk
## 331 0.09114939 331 0.09375152 Age1wk - Age4wk
## 332 0.16594965 332 0.17200603 Age1wk - Age4wk
## 333 0.09114939 333 0.10045006 Age1wk - Age4wk
## 334 1.00000000 334 1.00000000 Age1wk - Age4wk
## 335 0.10297068 335 0.10765200 Age1wk - Age4wk
## 336 0.09114939 336 0.09375152 Age1wk - Age4wk
## 337 0.49258414 337 0.50496245 Age1wk - Age4wk
## 338 0.87980301 338 0.88256211 Age1wk - Age4wk
## 339 1.00000000 339 1.00000000 Age1wk - Age4wk
## 340 1.00000000 340 1.00000000 Age1wk - Age4wk
## 341 1.00000000 341 1.00000000 Age1wk - Age4wk
## 342 1.00000000 342 1.00000000 Age1wk - Age4wk
## 343 0.92578110 343 0.92643911 Age1wk - Age4wk
## 344 0.98357111 344 0.99454290 Age1wk - Age4wk
## 345 0.21349356 345 0.21425166 Age1wk - Age4wk
## 346 0.56725809 346 0.57227860 Age1wk - Age4wk
## 347 1.00000000 347 1.00000000 Age1wk - Age4wk
## 348 1.00000000 348 1.00000000 Age1wk - Age4wk
## 349 0.68658378 349 0.70109158 Age1wk - Age4wk
## 350 0.60285081 350 0.61521340 Age1wk - Age4wk
## 351 0.20839744 351 0.20893591 Age1wk - Age4wk
## 352 0.82626071 352 0.82906487 Age1wk - Age4wk
## 353 0.09114939 353 0.10045006 Age1wk - Age4wk
## 354 0.85370086 354 0.85440395 Age1wk - Age4wk
## 355 0.53251966 355 0.54862198 Age1wk - Age4wk
## 356 0.94631975 356 0.95000490 Age1wk - Age4wk
## 357 0.23471308 357 0.23383778 Age1wk - Age4wk
## 358 0.18844309 358 0.19283769 Age1wk - Age4wk
## 359 1.00000000 359 1.00000000 Age1wk - Age4wk
## 360 0.18844309 360 0.19283769 Age1wk - Age4wk
## 361 0.99395278 361 1.00000000 Age1wk - Age4wk
## 362 0.54522911 362 0.56319268 Age1wk - Age4wk
## 363 0.11955874 363 0.12999020 Age1wk - Age4wk
## 364 0.71147119 364 0.72776145 Age1wk - Age4wk
## 365 0.63572089 365 0.64312065 Age1wk - Age4wk
## 366 0.37565766 366 0.37131440 Age1wk - Age4wk
## PValue_adj_withinNhood
## 1 0.4210253845
## 2 0.0791879438
## 3 0.7612127132
## 4 0.1163473638
## 5 0.0507090901
## 6 0.2708994749
## 7 0.3866062173
## 8 0.1198385389
## 9 0.9676843442
## 10 0.0040238627
## 11 0.2586529492
## 12 0.3135274330
## 13 0.2623791367
## 14 0.4309279424
## 15 0.8749909807
## 16 1.0000000000
## 17 0.9004412283
## 18 0.2387063266
## 19 0.3329743580
## 20 0.0772423580
## 21 0.1577769278
## 22 0.0643335849
## 23 0.3928441499
## 24 0.1024907363
## 25 0.0487078683
## 26 0.0081068544
## 27 0.9975727284
## 28 0.9377381769
## 29 0.6550982620
## 30 0.5690427236
## 31 0.3745861439
## 32 0.3185361078
## 33 0.7866279704
## 34 0.7632081809
## 35 0.7948212664
## 36 0.2459215202
## 37 1.0000000000
## 38 0.0239879511
## 39 0.3599976255
## 40 0.1166016755
## 41 0.7342443136
## 42 0.8431740949
## 43 0.6566819714
## 44 0.1657571817
## 45 0.8759785037
## 46 0.0968393657
## 47 0.0234689461
## 48 1.0000000000
## 49 0.6116341342
## 50 1.0000000000
## 51 0.0702802771
## 52 0.0755499959
## 53 0.0930371424
## 54 0.6217770989
## 55 0.8085700929
## 56 0.0817112190
## 57 0.4224142763
## 58 0.5166066781
## 59 0.9686297158
## 60 0.4341616628
## 61 0.9325867996
## 62 1.0000000000
## 63 0.1129025742
## 64 0.0631980623
## 65 0.2387063266
## 66 0.0047317991
## 67 1.0000000000
## 68 0.5413034164
## 69 0.0447084452
## 70 0.2676088827
## 71 0.4334044691
## 72 0.0391657633
## 73 1.0000000000
## 74 0.4121089950
## 75 0.2671710214
## 76 1.0000000000
## 77 0.0094732333
## 78 1.0000000000
## 79 0.9275701361
## 80 0.3324687347
## 81 0.0044926275
## 82 0.0162484649
## 83 0.1070026247
## 84 0.0204581929
## 85 0.1234005721
## 86 0.3935677605
## 87 0.0424183386
## 88 1.0000000000
## 89 1.0000000000
## 90 1.0000000000
## 91 0.4901871882
## 92 1.0000000000
## 93 0.2713246035
## 94 0.6975431036
## 95 0.3658028354
## 96 0.0046196980
## 97 0.1261249260
## 98 0.0024012824
## 99 0.1326218392
## 100 0.3794934127
## 101 0.0012564392
## 102 0.3586670090
## 103 0.0102821675
## 104 0.0082160337
## 105 0.2412788996
## 106 0.3767102775
## 107 1.0000000000
## 108 1.0000000000
## 109 0.3187823160
## 110 0.2137070806
## 111 0.4853168412
## 112 0.1388934736
## 113 0.1034902775
## 114 0.0558762073
## 115 0.0820375496
## 116 0.6694202121
## 117 0.8826423306
## 118 0.2614213803
## 119 0.4904227708
## 120 0.6875028854
## 121 0.8835776929
## 122 1.0000000000
## 123 0.0803408894
## 124 0.7517842324
## 125 0.9167360152
## 126 0.4857198005
## 127 0.7452721403
## 128 0.7149027621
## 129 0.1620472648
## 130 0.2966575199
## 131 0.2480272764
## 132 0.1299673636
## 133 0.0111437756
## 134 0.0164824923
## 135 0.2387063266
## 136 0.0250384492
## 137 0.0256800896
## 138 1.0000000000
## 139 0.6480271386
## 140 0.7288878198
## 141 1.0000000000
## 142 0.7957053668
## 143 0.2594510374
## 144 1.0000000000
## 145 1.0000000000
## 146 0.7267345380
## 147 0.7948028036
## 148 0.0033935021
## 149 0.3137767370
## 150 0.3999446988
## 151 0.0221216622
## 152 0.3980826609
## 153 1.0000000000
## 154 0.1247992388
## 155 0.5883071019
## 156 0.9224239331
## 157 0.0040859793
## 158 0.0080747600
## 159 0.0217140598
## 160 0.1039572843
## 161 0.5828178487
## 162 0.3575087190
## 163 0.0164881563
## 164 0.2568457024
## 165 0.4618480113
## 166 0.0156294863
## 167 0.0392880415
## 168 0.6054411249
## 169 0.2103234386
## 170 0.0030391116
## 171 0.9464485335
## 172 0.0265193144
## 173 0.6809636743
## 174 0.2547231745
## 175 0.2847862832
## 176 0.6080993973
## 177 0.8389101085
## 178 0.6239682822
## 179 0.9863917980
## 180 0.6561035392
## 181 1.0000000000
## 182 0.3830449019
## 183 0.0135854904
## 184 0.2619882122
## 185 0.0153559032
## 186 0.0542553613
## 187 0.2387063266
## 188 0.0072146190
## 189 0.6445461335
## 190 0.0085203735
## 191 1.0000000000
## 192 0.0007766992
## 193 0.1305281065
## 194 0.4469540639
## 195 0.2417277227
## 196 0.0059081539
## 197 0.4598882088
## 198 0.4974841771
## 199 1.0000000000
## 200 0.6287260829
## 201 0.0246465740
## 202 0.2032340829
## 203 0.4300056455
## 204 0.0584705193
## 205 0.4106355889
## 206 0.0356193934
## 207 0.0214939042
## 208 0.6943789163
## 209 0.2593878772
## 210 0.8039092163
## 211 0.1060463785
## 212 1.0000000000
## 213 0.0277624728
## 214 0.7133425905
## 215 0.3129224078
## 216 0.1886814275
## 217 0.4285575619
## 218 0.0173039763
## 219 0.5326491365
## 220 0.5354549968
## 221 0.0408641707
## 222 0.1685800248
## 223 0.7487910112
## 224 0.7769198177
## 225 0.2278523568
## 226 0.9325646033
## 227 0.0427852402
## 228 0.8808429823
## 229 0.0109124983
## 230 0.9973410612
## 231 0.7339011375
## 232 0.7139655556
## 233 0.3989601298
## 234 1.0000000000
## 235 0.4009539803
## 236 0.7947279933
## 237 0.3454561771
## 238 1.0000000000
## 239 0.2387063266
## 240 1.0000000000
## 241 0.1184087562
## 242 1.0000000000
## 243 0.0629626136
## 244 0.9044840102
## 245 1.0000000000
## 246 0.1748954459
## 247 1.0000000000
## 248 0.6457238375
## 249 0.0268561470
## 250 0.0976670854
## 251 0.2475094293
## 252 0.3360580106
## 253 0.0769635029
## 254 0.3840867967
## 255 0.2387063266
## 256 0.1371392138
## 257 0.1559376606
## 258 0.5574713238
## 259 0.6516841777
## 260 0.0566512431
## 261 0.2387063272
## 262 1.0000000000
## 263 0.0256809397
## 264 0.0009340067
## 265 0.1258046843
## 266 0.7700648305
## 267 1.0000000000
## 268 0.1219583356
## 269 0.0079596767
## 270 0.0251617532
## 271 0.0031543984
## 272 1.0000000000
## 273 0.7857957571
## 274 0.1074764853
## 275 0.5896214022
## 276 0.2387063266
## 277 0.1287117527
## 278 0.2440284839
## 279 0.5693658859
## 280 0.7570350121
## 281 0.0275940954
## 282 0.4837001033
## 283 0.0788350647
## 284 0.0016854662
## 285 0.3726410302
## 286 0.0378797386
## 287 0.0173153442
## 288 0.4675060542
## 289 1.0000000000
## 290 0.5485760509
## 291 0.1180557523
## 292 0.0644493011
## 293 0.6590343481
## 294 0.6997176131
## 295 0.0518864394
## 296 0.0036781233
## 297 0.0589770250
## 298 0.0245770666
## 299 0.2606307412
## 300 0.2634805331
## 301 0.9865020155
## 302 0.9747448835
## 303 0.1216636414
## 304 0.1046183723
## 305 0.0174675738
## 306 0.0358305705
## 307 0.5790972428
## 308 1.0000000000
## 309 0.5287049263
## 310 0.0961013186
## 311 0.2387063277
## 312 1.0000000000
## 313 0.2592314951
## 314 0.3085965215
## 315 0.6179657320
## 316 0.0022848286
## 317 0.3253021431
## 318 0.1094582567
## 319 0.9700200727
## 320 0.0105667494
## 321 0.4106422400
## 322 0.3116400508
## 323 0.2312492234
## 324 0.0258446175
## 325 0.8610790285
## 326 0.2387063266
## 327 0.7244238134
## 328 0.0212495571
## 329 0.8962675296
## 330 0.4191797755
## 331 0.0015199879
## 332 0.0251159423
## 333 0.0021680700
## 334 1.0000000000
## 335 0.0056471447
## 336 0.0010077043
## 337 0.1803450124
## 338 0.5913430066
## 339 1.0000000000
## 340 0.9969297217
## 341 1.0000000000
## 342 1.0000000000
## 343 0.6627176203
## 344 0.7612896937
## 345 0.0414154176
## 346 0.2358971382
## 347 0.9716313323
## 348 1.0000000000
## 349 0.3657579124
## 350 0.2898954730
## 351 0.0390686948
## 352 0.5237499587
## 353 0.0030010651
## 354 0.5559665608
## 355 0.1978761588
## 356 0.6877624448
## 357 0.0487382350
## 358 0.0320943899
## 359 1.0000000000
## 360 0.0324369260
## 361 0.7936106721
## 362 0.2055781901
## 363 0.0092790325
## 364 0.4067066355
## 365 0.3213343320
## 366 0.1122794624
##
## $artifacts$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] 366
##
## $summary$n_samples
## [1] 25
##
##
## $created_at
## [1] "2026-06-15 03:50:48 UTC"
##
## $da_results
## logFC logCPM F PValue
## 1 1.05935398 13.68486 6.475242e-01 0.4210253845
## 2 -2.37707947 13.42732 3.082349e+00 0.0791879438
## 3 -0.39265998 13.60684 9.235521e-02 0.7612127132
## 4 -2.12054771 13.50604 2.466399e+00 0.1163473638
## 5 -2.70915344 13.58856 3.819113e+00 0.0507090901
## 6 -1.53019896 13.68581 1.212370e+00 0.2708994749
## 7 1.09599128 13.59844 7.496791e-01 0.3866062173
## 8 -2.06475222 13.57967 2.419995e+00 0.1198385389
## 9 -0.04560136 13.39561 1.641395e-03 0.9676843442
## 10 -4.07040881 13.41032 8.278258e+00 0.0040238627
## 11 1.19921557 13.75236 1.276151e+00 0.2586529492
## 12 -1.29745201 13.46307 1.015897e+00 0.3135274330
## 13 -1.20542395 13.67260 1.256354e+00 0.2623791367
## 14 -0.98814968 13.43876 6.203899e-01 0.4309279424
## 15 0.20025829 13.75932 2.475198e-02 0.8749909807
## 16 0.00000000 13.69412 0.000000e+00 1.0000000000
## 17 -0.15379327 13.43376 1.565209e-02 0.9004412283
## 18 -1.31601366 13.46775 1.409391e+00 0.2387063266
## 19 1.21427610 13.50690 9.374195e-01 0.3329743580
## 20 2.43410452 13.70102 3.122870e+00 0.0772423580
## 21 1.77377154 13.56292 1.995813e+00 0.1577769278
## 22 -2.36844178 13.45807 3.423020e+00 0.0643335849
## 23 -1.14373521 13.68938 7.302067e-01 0.3928441499
## 24 2.23367648 13.66217 2.667019e+00 0.1024907363
## 25 -2.86408861 13.71473 3.886690e+00 0.0487078683
## 26 -3.72370108 13.53541 7.013553e+00 0.0081068544
## 27 0.07472994 13.32977 3.208742e-03 0.9975727284
## 28 -0.09909769 13.57336 6.102058e-03 0.9377381769
## 29 -0.55033324 13.45792 1.995491e-01 0.6550982620
## 30 -0.78270885 13.40775 3.243162e-01 0.5690427236
## 31 -1.16966589 13.41634 7.884905e-01 0.3745861439
## 32 -1.37930895 13.66319 9.950833e-01 0.3185361078
## 33 0.36089085 13.75338 7.327950e-02 0.7866279704
## 34 -0.40319522 13.63130 9.077072e-02 0.7632081809
## 35 0.32138321 13.39361 6.763359e-02 0.7948212664
## 36 -1.31810889 13.65063 1.346541e+00 0.2459215202
## 37 0.00000000 13.40337 0.000000e+00 1.0000000000
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## 334 0.00000000 13.34440 0.000000e+00 1.0000000000
## 335 -3.85810003 13.31546 7.664119e+00 0.0056471447
## 336 4.85734299 13.49811 1.082209e+01 0.0010077043
## 337 1.68893110 13.44329 1.795121e+00 0.1803450124
## 338 -0.69276032 13.37195 2.882772e-01 0.5913430066
## 339 0.00000000 13.69677 0.000000e+00 1.0000000000
## 340 -0.02501548 13.50882 3.953812e-04 0.9969297217
## 341 0.00000000 13.45008 0.000000e+00 1.0000000000
## 342 0.00000000 13.60730 0.000000e+00 1.0000000000
## 343 -0.55445052 13.44730 1.902547e-01 0.6627176203
## 344 -0.39768003 13.56373 9.229381e-02 0.7612896937
## 345 -2.66533027 13.41537 4.160402e+00 0.0414154176
## 346 -1.53135419 13.43140 1.405177e+00 0.2358971382
## 347 0.04777135 13.60026 1.264767e-03 0.9716313323
## 348 0.00000000 13.42919 0.000000e+00 1.0000000000
## 349 -1.14501930 13.56201 8.181277e-01 0.3657579124
## 350 -1.38791913 13.62033 1.120269e+00 0.2898954730
## 351 -2.72282957 13.45709 4.259408e+00 0.0390686948
## 352 -0.80832073 13.59047 4.065417e-01 0.5237499587
## 353 4.20578610 13.33058 8.812723e+00 0.0030010651
## 354 -0.73957639 13.33649 3.467680e-01 0.5559665608
## 355 -1.69864614 13.78526 1.658282e+00 0.1978761588
## 356 -0.51750240 13.58902 1.615312e-01 0.6877624448
## 357 -2.69003811 13.55936 3.885642e+00 0.0487382350
## 358 2.92737300 13.39231 4.595203e+00 0.0320943899
## 359 0.00000000 13.56163 0.000000e+00 1.0000000000
## 360 2.93998866 13.36697 4.576997e+00 0.0324369260
## 361 -0.33742206 13.45854 6.845257e-02 0.7936106721
## 362 -1.64541862 13.43326 1.602580e+00 0.2055781901
## 363 3.70461051 13.58793 6.771909e+00 0.0092790325
## 364 -1.08487452 13.44170 6.884867e-01 0.4067066355
## 365 -1.27136857 13.49282 9.836410e-01 0.3213343320
## 366 -2.13330917 13.55085 2.522447e+00 0.1122794624
## FDR Nhood SpatialFDR contrast
## 1 0.71908663 1 0.73606580 Age1wk - Age4wk
## 2 0.31164288 2 0.30949800 Age1wk - Age4wk
## 3 0.98357111 3 0.99454290 Age1wk - Age4wk
## 4 0.38015443 4 0.37624693 Age1wk - Age4wk
## 5 0.24103282 5 0.24095128 Age1wk - Age4wk
## 6 0.57071727 6 0.58315112 Age1wk - Age4wk
## 7 0.70048453 7 0.71842809 Age1wk - Age4wk
## 8 0.38139918 8 0.37766393 Age1wk - Age4wk
## 9 1.00000000 9 1.00000000 Age1wk - Age4wk
## 10 0.09114939 10 0.10045006 Age1wk - Age4wk
## 11 0.56725809 11 0.58077260 Age1wk - Age4wk
## 12 0.63100157 12 0.64312065 Age1wk - Age4wk
## 13 0.56725809 13 0.58077260 Age1wk - Age4wk
## 14 0.72228713 14 0.73606580 Age1wk - Age4wk
## 15 1.00000000 15 1.00000000 Age1wk - Age4wk
## 16 1.00000000 16 1.00000000 Age1wk - Age4wk
## 17 1.00000000 17 1.00000000 Age1wk - Age4wk
## 18 0.56725809 18 0.57227860 Age1wk - Age4wk
## 19 0.64823731 19 0.65862315 Age1wk - Age4wk
## 20 0.31066707 20 0.30949800 Age1wk - Age4wk
## 21 0.44764617 21 0.45690049 Age1wk - Age4wk
## 22 0.27113154 22 0.27283998 Age1wk - Age4wk
## 23 0.70552479 23 0.72585904 Age1wk - Age4wk
## 24 0.36762985 24 0.36523002 Age1wk - Age4wk
## 25 0.23471308 25 0.23383778 Age1wk - Age4wk
## 26 0.11549840 26 0.12101680 Age1wk - Age4wk
## 27 1.00000000 27 1.00000000 Age1wk - Age4wk
## 28 1.00000000 28 1.00000000 Age1wk - Age4wk
## 29 0.92416311 29 0.92233488 Age1wk - Age4wk
## 30 0.86468014 30 0.86756775 Age1wk - Age4wk
## 31 0.69593162 31 0.71128448 Age1wk - Age4wk
## 32 0.63409961 32 0.64312065 Age1wk - Age4wk
## 33 0.99395278 33 1.00000000 Age1wk - Age4wk
## 34 0.98357111 34 0.99503656 Age1wk - Age4wk
## 35 0.99395278 35 1.00000000 Age1wk - Age4wk
## 36 0.56725809 36 0.57491903 Age1wk - Age4wk
## 37 1.00000000 37 1.00000000 Age1wk - Age4wk
## 38 0.16594965 38 0.17200603 Age1wk - Age4wk
## 39 0.68268980 39 0.69494957 Age1wk - Age4wk
## 40 0.38015443 40 0.37624693 Age1wk - Age4wk
## 41 0.97015675 41 0.97773294 Age1wk - Age4wk
## 42 1.00000000 42 1.00000000 Age1wk - Age4wk
## 43 0.92416311 43 0.92233488 Age1wk - Age4wk
## 44 0.46310785 44 0.47528615 Age1wk - Age4wk
## 45 1.00000000 45 1.00000000 Age1wk - Age4wk
## 46 0.35746153 46 0.35826618 Age1wk - Age4wk
## 47 0.16594965 47 0.17200603 Age1wk - Age4wk
## 48 1.00000000 48 1.00000000 Age1wk - Age4wk
## 49 0.89902849 49 0.90366144 Age1wk - Age4wk
## 50 1.00000000 50 1.00000000 Age1wk - Age4wk
## 51 0.29230206 51 0.29360199 Age1wk - Age4wk
## 52 0.31066707 52 0.30856475 Age1wk - Age4wk
## 53 0.35104736 53 0.35036492 Age1wk - Age4wk
## 54 0.90623965 54 0.90436924 Age1wk - Age4wk
## 55 1.00000000 55 1.00000000 Age1wk - Age4wk
## 56 0.31276816 56 0.31045281 Age1wk - Age4wk
## 57 0.71908663 57 0.73606580 Age1wk - Age4wk
## 58 0.81851967 58 0.81965873 Age1wk - Age4wk
## 59 1.00000000 59 1.00000000 Age1wk - Age4wk
## 60 0.72228713 60 0.73606580 Age1wk - Age4wk
## 61 1.00000000 61 1.00000000 Age1wk - Age4wk
## 62 1.00000000 62 1.00000000 Age1wk - Age4wk
## 63 0.37565766 63 0.37131440 Age1wk - Age4wk
## 64 0.27113154 64 0.27283998 Age1wk - Age4wk
## 65 0.56725809 65 0.57227860 Age1wk - Age4wk
## 66 0.09114939 66 0.10045006 Age1wk - Age4wk
## 67 1.00000000 67 1.00000000 Age1wk - Age4wk
## 68 0.83947903 68 0.84553872 Age1wk - Age4wk
## 69 0.22112555 69 0.22013974 Age1wk - Age4wk
## 70 0.56944681 70 0.58185549 Age1wk - Age4wk
## 71 0.72228713 71 0.73606580 Age1wk - Age4wk
## 72 0.20839744 72 0.20893591 Age1wk - Age4wk
## 73 1.00000000 73 1.00000000 Age1wk - Age4wk
## 74 0.71147119 74 0.72776145 Age1wk - Age4wk
## 75 0.56944681 75 0.58185549 Age1wk - Age4wk
## 76 1.00000000 76 1.00000000 Age1wk - Age4wk
## 77 0.11955874 77 0.12999020 Age1wk - Age4wk
## 78 1.00000000 78 1.00000000 Age1wk - Age4wk
## 79 1.00000000 79 1.00000000 Age1wk - Age4wk
## 80 0.64823731 80 0.65862315 Age1wk - Age4wk
## 81 0.09114939 81 0.10045006 Age1wk - Age4wk
## 82 0.15221743 82 0.16460008 Age1wk - Age4wk
## 83 0.36762985 83 0.36523002 Age1wk - Age4wk
## 84 0.16594965 84 0.17200603 Age1wk - Age4wk
## 85 0.38150184 85 0.38136289 Age1wk - Age4wk
## 86 0.70552479 86 0.72585904 Age1wk - Age4wk
## 87 0.21451230 87 0.21443720 Age1wk - Age4wk
## 88 1.00000000 88 1.00000000 Age1wk - Age4wk
## 89 1.00000000 89 1.00000000 Age1wk - Age4wk
## 90 1.00000000 90 1.00000000 Age1wk - Age4wk
## 91 0.78381980 91 0.79266407 Age1wk - Age4wk
## 92 1.00000000 92 1.00000000 Age1wk - Age4wk
## 93 0.57071727 93 0.58315112 Age1wk - Age4wk
## 94 0.95203214 94 0.95709869 Age1wk - Age4wk
## 95 0.68658378 95 0.70109158 Age1wk - Age4wk
## 96 0.09114939 96 0.10045006 Age1wk - Age4wk
## 97 0.38150184 97 0.38143543 Age1wk - Age4wk
## 98 0.09114939 98 0.10045006 Age1wk - Age4wk
## 99 0.38831675 99 0.39283690 Age1wk - Age4wk
## 100 0.69796276 100 0.71499691 Age1wk - Age4wk
## 101 0.09114939 101 0.09375152 Age1wk - Age4wk
## 102 0.68268980 102 0.69494957 Age1wk - Age4wk
## 103 0.12359460 103 0.13846980 Age1wk - Age4wk
## 104 0.11549840 104 0.12101680 Age1wk - Age4wk
## 105 0.56725809 105 0.57227860 Age1wk - Age4wk
## 106 0.69634324 106 0.71250721 Age1wk - Age4wk
## 107 1.00000000 107 1.00000000 Age1wk - Age4wk
## 108 1.00000000 108 1.00000000 Age1wk - Age4wk
## 109 0.63409961 109 0.64312065 Age1wk - Age4wk
## 110 0.55869137 110 0.57227860 Age1wk - Age4wk
## 111 0.78314294 111 0.79100271 Age1wk - Age4wk
## 112 0.40027568 112 0.40715956 Age1wk - Age4wk
## 113 0.36762985 113 0.36523002 Age1wk - Age4wk
## 114 0.25563365 114 0.25654278 Age1wk - Age4wk
## 115 0.31276816 115 0.31045281 Age1wk - Age4wk
## 116 0.93158858 116 0.93235877 Age1wk - Age4wk
## 117 1.00000000 117 1.00000000 Age1wk - Age4wk
## 118 0.56725809 118 0.58077260 Age1wk - Age4wk
## 119 0.78381980 119 0.79266407 Age1wk - Age4wk
## 120 0.94631975 120 0.95000490 Age1wk - Age4wk
## 121 1.00000000 121 1.00000000 Age1wk - Age4wk
## 122 1.00000000 122 1.00000000 Age1wk - Age4wk
## 123 0.31276816 123 0.31024932 Age1wk - Age4wk
## 124 0.98268939 124 0.99223946 Age1wk - Age4wk
## 125 1.00000000 125 1.00000000 Age1wk - Age4wk
## 126 0.78314294 126 0.79100271 Age1wk - Age4wk
## 127 0.98118562 127 0.99046770 Age1wk - Age4wk
## 128 0.96196475 128 0.96913640 Age1wk - Age4wk
## 129 0.45622538 129 0.46596150 Age1wk - Age4wk
## 130 0.61342741 130 0.62653297 Age1wk - Age4wk
## 131 0.56725809 131 0.57575383 Age1wk - Age4wk
## 132 0.38526844 132 0.38890436 Age1wk - Age4wk
## 133 0.12359460 133 0.13987381 Age1wk - Age4wk
## 134 0.15221743 134 0.16460008 Age1wk - Age4wk
## 135 0.56725809 135 0.57227860 Age1wk - Age4wk
## 136 0.16594965 136 0.17200603 Age1wk - Age4wk
## 137 0.16594965 137 0.17200603 Age1wk - Age4wk
## 138 1.00000000 138 1.00000000 Age1wk - Age4wk
## 139 0.92416311 139 0.92007578 Age1wk - Age4wk
## 140 0.97008343 140 0.97435595 Age1wk - Age4wk
## 141 1.00000000 141 1.00000000 Age1wk - Age4wk
## 142 0.99395278 142 1.00000000 Age1wk - Age4wk
## 143 0.56725809 143 0.58077260 Age1wk - Age4wk
## 144 1.00000000 144 1.00000000 Age1wk - Age4wk
## 145 1.00000000 145 1.00000000 Age1wk - Age4wk
## 146 0.97008343 146 0.97435595 Age1wk - Age4wk
## 147 0.99395278 147 1.00000000 Age1wk - Age4wk
## 148 0.09114939 148 0.10045006 Age1wk - Age4wk
## 149 0.63100157 149 0.64312065 Age1wk - Age4wk
## 150 0.70552479 150 0.72585904 Age1wk - Age4wk
## 151 0.16594965 151 0.17200603 Age1wk - Age4wk
## 152 0.70552479 152 0.72585904 Age1wk - Age4wk
## 153 1.00000000 153 1.00000000 Age1wk - Age4wk
## 154 0.38150184 154 0.38143543 Age1wk - Age4wk
## 155 0.87980301 155 0.88256211 Age1wk - Age4wk
## 156 1.00000000 156 1.00000000 Age1wk - Age4wk
## 157 0.09114939 157 0.10045006 Age1wk - Age4wk
## 158 0.11549840 158 0.12101680 Age1wk - Age4wk
## 159 0.16594965 159 0.17200603 Age1wk - Age4wk
## 160 0.36762985 160 0.36523002 Age1wk - Age4wk
## 161 0.87782441 161 0.88093908 Age1wk - Age4wk
## 162 0.68268980 162 0.69494957 Age1wk - Age4wk
## 163 0.15221743 163 0.16460008 Age1wk - Age4wk
## 164 0.56725809 164 0.58077260 Age1wk - Age4wk
## 165 0.75801064 165 0.76743784 Age1wk - Age4wk
## 166 0.15221743 166 0.16460008 Age1wk - Age4wk
## 167 0.20839744 167 0.20893591 Age1wk - Age4wk
## 168 0.89713138 168 0.89871130 Age1wk - Age4wk
## 169 0.55380128 169 0.57143469 Age1wk - Age4wk
## 170 0.09114939 170 0.10045006 Age1wk - Age4wk
## 171 1.00000000 171 1.00000000 Age1wk - Age4wk
## 172 0.16657484 172 0.17200603 Age1wk - Age4wk
## 173 0.94406328 173 0.94597913 Age1wk - Age4wk
## 174 0.56725809 174 0.58077260 Age1wk - Age4wk
## 175 0.59561017 175 0.60614481 Age1wk - Age4wk
## 176 0.89743701 176 0.90124072 Age1wk - Age4wk
## 177 1.00000000 177 1.00000000 Age1wk - Age4wk
## 178 0.90623965 178 0.90436924 Age1wk - Age4wk
## 179 1.00000000 179 1.00000000 Age1wk - Age4wk
## 180 0.92416311 180 0.92233488 Age1wk - Age4wk
## 181 1.00000000 181 1.00000000 Age1wk - Age4wk
## 182 0.69938193 182 0.71634713 Age1wk - Age4wk
## 183 0.14624381 183 0.16414179 Age1wk - Age4wk
## 184 0.56725809 184 0.58077260 Age1wk - Age4wk
## 185 0.15221743 185 0.16460008 Age1wk - Age4wk
## 186 0.25136028 186 0.25291250 Age1wk - Age4wk
## 187 0.56725809 187 0.57227860 Age1wk - Age4wk
## 188 0.11549840 188 0.12101680 Age1wk - Age4wk
## 189 0.92416311 189 0.91910842 Age1wk - Age4wk
## 190 0.11549840 190 0.12247835 Age1wk - Age4wk
## 191 1.00000000 191 1.00000000 Age1wk - Age4wk
## 192 0.09114939 192 0.09375152 Age1wk - Age4wk
## 193 0.38526844 193 0.38902902 Age1wk - Age4wk
## 194 0.74020447 194 0.75560835 Age1wk - Age4wk
## 195 0.56725809 195 0.57227860 Age1wk - Age4wk
## 196 0.10297068 196 0.10765200 Age1wk - Age4wk
## 197 0.75801064 197 0.76743784 Age1wk - Age4wk
## 198 0.79164873 198 0.80028649 Age1wk - Age4wk
## 199 1.00000000 199 1.00000000 Age1wk - Age4wk
## 200 0.90954050 200 0.90901274 Age1wk - Age4wk
## 201 0.16594965 201 0.17200603 Age1wk - Age4wk
## 202 0.54294653 202 0.56047672 Age1wk - Age4wk
## 203 0.72228713 203 0.73606580 Age1wk - Age4wk
## 204 0.26006736 204 0.26017165 Age1wk - Age4wk
## 205 0.71147119 205 0.72776145 Age1wk - Age4wk
## 206 0.20175367 206 0.20411658 Age1wk - Age4wk
## 207 0.16594965 207 0.17200603 Age1wk - Age4wk
## 208 0.95184526 208 0.95570524 Age1wk - Age4wk
## 209 0.56725809 209 0.58077260 Age1wk - Age4wk
## 210 1.00000000 210 1.00000000 Age1wk - Age4wk
## 211 0.36762985 211 0.36523002 Age1wk - Age4wk
## 212 1.00000000 212 1.00000000 Age1wk - Age4wk
## 213 0.16657484 213 0.17200603 Age1wk - Age4wk
## 214 0.96196475 214 0.96913640 Age1wk - Age4wk
## 215 0.63100157 215 0.64312065 Age1wk - Age4wk
## 216 0.51153631 216 0.52578743 Age1wk - Age4wk
## 217 0.72228713 217 0.73606580 Age1wk - Age4wk
## 218 0.15221743 218 0.16460008 Age1wk - Age4wk
## 219 0.83311788 219 0.83757160 Age1wk - Age4wk
## 220 0.83394268 220 0.83782566 Age1wk - Age4wk
## 221 0.21349356 221 0.21425166 Age1wk - Age4wk
## 222 0.46742643 222 0.47948987 Age1wk - Age4wk
## 223 0.98228498 223 0.99223946 Age1wk - Age4wk
## 224 0.99395278 224 1.00000000 Age1wk - Age4wk
## 225 0.56725809 225 0.57227860 Age1wk - Age4wk
## 226 1.00000000 226 1.00000000 Age1wk - Age4wk
## 227 0.21451230 227 0.21443720 Age1wk - Age4wk
## 228 1.00000000 228 1.00000000 Age1wk - Age4wk
## 229 0.12359460 229 0.13985179 Age1wk - Age4wk
## 230 1.00000000 230 1.00000000 Age1wk - Age4wk
## 231 0.97015675 231 0.97773294 Age1wk - Age4wk
## 232 0.96196475 232 0.96913640 Age1wk - Age4wk
## 233 0.70552479 233 0.72585904 Age1wk - Age4wk
## 234 1.00000000 234 1.00000000 Age1wk - Age4wk
## 235 0.70552479 235 0.72585904 Age1wk - Age4wk
## 236 0.99395278 236 1.00000000 Age1wk - Age4wk
## 237 0.66545769 237 0.67605524 Age1wk - Age4wk
## 238 1.00000000 238 1.00000000 Age1wk - Age4wk
## 239 0.56725809 239 0.57227860 Age1wk - Age4wk
## 240 1.00000000 240 1.00000000 Age1wk - Age4wk
## 241 0.38015443 241 0.37624693 Age1wk - Age4wk
## 242 1.00000000 242 1.00000000 Age1wk - Age4wk
## 243 0.27113154 243 0.27283998 Age1wk - Age4wk
## 244 1.00000000 244 1.00000000 Age1wk - Age4wk
## 245 1.00000000 245 1.00000000 Age1wk - Age4wk
## 246 0.48129123 246 0.49354784 Age1wk - Age4wk
## 247 1.00000000 247 1.00000000 Age1wk - Age4wk
## 248 0.92416311 248 0.91910842 Age1wk - Age4wk
## 249 0.16657484 249 0.17200603 Age1wk - Age4wk
## 250 0.35746153 250 0.35826618 Age1wk - Age4wk
## 251 0.56725809 251 0.57575383 Age1wk - Age4wk
## 252 0.65077900 252 0.66200231 Age1wk - Age4wk
## 253 0.31066707 253 0.30949800 Age1wk - Age4wk
## 254 0.69938193 254 0.71634713 Age1wk - Age4wk
## 255 0.56725809 255 0.57227860 Age1wk - Age4wk
## 256 0.39835676 256 0.40425253 Age1wk - Age4wk
## 257 0.44588425 257 0.45329772 Age1wk - Age4wk
## 258 0.85370086 258 0.85440395 Age1wk - Age4wk
## 259 0.92416311 259 0.92233488 Age1wk - Age4wk
## 260 0.25597969 260 0.25664782 Age1wk - Age4wk
## 261 0.56725809 261 0.57227860 Age1wk - Age4wk
## 262 1.00000000 262 1.00000000 Age1wk - Age4wk
## 263 0.16594965 263 0.17200603 Age1wk - Age4wk
## 264 0.09114939 264 0.09375152 Age1wk - Age4wk
## 265 0.38150184 265 0.38143543 Age1wk - Age4wk
## 266 0.98892536 266 0.99876360 Age1wk - Age4wk
## 267 1.00000000 267 1.00000000 Age1wk - Age4wk
## 268 0.38150184 268 0.37859013 Age1wk - Age4wk
## 269 0.11549840 269 0.12101680 Age1wk - Age4wk
## 270 0.16594965 270 0.17200603 Age1wk - Age4wk
## 271 0.09114939 271 0.10045006 Age1wk - Age4wk
## 272 1.00000000 272 1.00000000 Age1wk - Age4wk
## 273 0.99395278 273 1.00000000 Age1wk - Age4wk
## 274 0.36762985 274 0.36523002 Age1wk - Age4wk
## 275 0.87980301 275 0.88256211 Age1wk - Age4wk
## 276 0.56725809 276 0.57227860 Age1wk - Age4wk
## 277 0.38526844 277 0.38716991 Age1wk - Age4wk
## 278 0.56725809 278 0.57227860 Age1wk - Age4wk
## 279 0.86468014 279 0.86756775 Age1wk - Age4wk
## 280 0.98357111 280 0.99454290 Age1wk - Age4wk
## 281 0.16657484 281 0.17200603 Age1wk - Age4wk
## 282 0.78314294 282 0.79100271 Age1wk - Age4wk
## 283 0.31164288 283 0.30949800 Age1wk - Age4wk
## 284 0.09114939 284 0.09375152 Age1wk - Age4wk
## 285 0.69585009 285 0.71128448 Age1wk - Age4wk
## 286 0.20839744 286 0.20893591 Age1wk - Age4wk
## 287 0.15221743 287 0.16460008 Age1wk - Age4wk
## 288 0.76387150 288 0.77300676 Age1wk - Age4wk
## 289 1.00000000 289 1.00000000 Age1wk - Age4wk
## 290 0.84716808 290 0.85292331 Age1wk - Age4wk
## 291 0.38015443 291 0.37624693 Age1wk - Age4wk
## 292 0.27113154 292 0.27283998 Age1wk - Age4wk
## 293 0.92416311 293 0.92375449 Age1wk - Age4wk
## 294 0.95203214 294 0.95844726 Age1wk - Age4wk
## 295 0.24346714 295 0.24321808 Age1wk - Age4wk
## 296 0.09114939 296 0.10045006 Age1wk - Age4wk
## 297 0.26006736 297 0.26057792 Age1wk - Age4wk
## 298 0.16594965 298 0.17200603 Age1wk - Age4wk
## 299 0.56725809 299 0.58077260 Age1wk - Age4wk
## 300 0.56725809 300 0.58077260 Age1wk - Age4wk
## 301 1.00000000 301 1.00000000 Age1wk - Age4wk
## 302 1.00000000 302 1.00000000 Age1wk - Age4wk
## 303 0.38150184 303 0.37859013 Age1wk - Age4wk
## 304 0.36762985 304 0.36523002 Age1wk - Age4wk
## 305 0.15221743 305 0.16460008 Age1wk - Age4wk
## 306 0.20175367 306 0.20411658 Age1wk - Age4wk
## 307 0.87582476 307 0.87729377 Age1wk - Age4wk
## 308 1.00000000 308 1.00000000 Age1wk - Age4wk
## 309 0.83049787 309 0.83502193 Age1wk - Age4wk
## 310 0.35746153 310 0.35826618 Age1wk - Age4wk
## 311 0.56725809 311 0.57227860 Age1wk - Age4wk
## 312 1.00000000 312 1.00000000 Age1wk - Age4wk
## 313 0.56725809 313 0.58077260 Age1wk - Age4wk
## 314 0.63100157 314 0.64312065 Age1wk - Age4wk
## 315 0.90470183 315 0.90436924 Age1wk - Age4wk
## 316 0.09114939 316 0.10045006 Age1wk - Age4wk
## 317 0.64011067 317 0.64719669 Age1wk - Age4wk
## 318 0.37094187 318 0.36523002 Age1wk - Age4wk
## 319 1.00000000 319 1.00000000 Age1wk - Age4wk
## 320 0.12359460 320 0.13873674 Age1wk - Age4wk
## 321 0.71147119 321 0.72776145 Age1wk - Age4wk
## 322 0.63100157 322 0.64312065 Age1wk - Age4wk
## 323 0.56725809 323 0.57227860 Age1wk - Age4wk
## 324 0.16594965 324 0.17200603 Age1wk - Age4wk
## 325 1.00000000 325 1.00000000 Age1wk - Age4wk
## 326 0.56725809 326 0.57227860 Age1wk - Age4wk
## 327 0.97008343 327 0.97435595 Age1wk - Age4wk
## 328 0.16594965 328 0.17200603 Age1wk - Age4wk
## 329 1.00000000 329 1.00000000 Age1wk - Age4wk
## 330 0.71908663 330 0.73606580 Age1wk - Age4wk
## 331 0.09114939 331 0.09375152 Age1wk - Age4wk
## 332 0.16594965 332 0.17200603 Age1wk - Age4wk
## 333 0.09114939 333 0.10045006 Age1wk - Age4wk
## 334 1.00000000 334 1.00000000 Age1wk - Age4wk
## 335 0.10297068 335 0.10765200 Age1wk - Age4wk
## 336 0.09114939 336 0.09375152 Age1wk - Age4wk
## 337 0.49258414 337 0.50496245 Age1wk - Age4wk
## 338 0.87980301 338 0.88256211 Age1wk - Age4wk
## 339 1.00000000 339 1.00000000 Age1wk - Age4wk
## 340 1.00000000 340 1.00000000 Age1wk - Age4wk
## 341 1.00000000 341 1.00000000 Age1wk - Age4wk
## 342 1.00000000 342 1.00000000 Age1wk - Age4wk
## 343 0.92578110 343 0.92643911 Age1wk - Age4wk
## 344 0.98357111 344 0.99454290 Age1wk - Age4wk
## 345 0.21349356 345 0.21425166 Age1wk - Age4wk
## 346 0.56725809 346 0.57227860 Age1wk - Age4wk
## 347 1.00000000 347 1.00000000 Age1wk - Age4wk
## 348 1.00000000 348 1.00000000 Age1wk - Age4wk
## 349 0.68658378 349 0.70109158 Age1wk - Age4wk
## 350 0.60285081 350 0.61521340 Age1wk - Age4wk
## 351 0.20839744 351 0.20893591 Age1wk - Age4wk
## 352 0.82626071 352 0.82906487 Age1wk - Age4wk
## 353 0.09114939 353 0.10045006 Age1wk - Age4wk
## 354 0.85370086 354 0.85440395 Age1wk - Age4wk
## 355 0.53251966 355 0.54862198 Age1wk - Age4wk
## 356 0.94631975 356 0.95000490 Age1wk - Age4wk
## 357 0.23471308 357 0.23383778 Age1wk - Age4wk
## 358 0.18844309 358 0.19283769 Age1wk - Age4wk
## 359 1.00000000 359 1.00000000 Age1wk - Age4wk
## 360 0.18844309 360 0.19283769 Age1wk - Age4wk
## 361 0.99395278 361 1.00000000 Age1wk - Age4wk
## 362 0.54522911 362 0.56319268 Age1wk - Age4wk
## 363 0.11955874 363 0.12999020 Age1wk - Age4wk
## 364 0.71147119 364 0.72776145 Age1wk - Age4wk
## 365 0.63572089 365 0.64312065 Age1wk - Age4wk
## 366 0.37565766 366 0.37131440 Age1wk - Age4wk
## PValue_adj_withinNhood
## 1 0.4210253845
## 2 0.0791879438
## 3 0.7612127132
## 4 0.1163473638
## 5 0.0507090901
## 6 0.2708994749
## 7 0.3866062173
## 8 0.1198385389
## 9 0.9676843442
## 10 0.0040238627
## 11 0.2586529492
## 12 0.3135274330
## 13 0.2623791367
## 14 0.4309279424
## 15 0.8749909807
## 16 1.0000000000
## 17 0.9004412283
## 18 0.2387063266
## 19 0.3329743580
## 20 0.0772423580
## 21 0.1577769278
## 22 0.0643335849
## 23 0.3928441499
## 24 0.1024907363
## 25 0.0487078683
## 26 0.0081068544
## 27 0.9975727284
## 28 0.9377381769
## 29 0.6550982620
## 30 0.5690427236
## 31 0.3745861439
## 32 0.3185361078
## 33 0.7866279704
## 34 0.7632081809
## 35 0.7948212664
## 36 0.2459215202
## 37 1.0000000000
## 38 0.0239879511
## 39 0.3599976255
## 40 0.1166016755
## 41 0.7342443136
## 42 0.8431740949
## 43 0.6566819714
## 44 0.1657571817
## 45 0.8759785037
## 46 0.0968393657
## 47 0.0234689461
## 48 1.0000000000
## 49 0.6116341342
## 50 1.0000000000
## 51 0.0702802771
## 52 0.0755499959
## 53 0.0930371424
## 54 0.6217770989
## 55 0.8085700929
## 56 0.0817112190
## 57 0.4224142763
## 58 0.5166066781
## 59 0.9686297158
## 60 0.4341616628
## 61 0.9325867996
## 62 1.0000000000
## 63 0.1129025742
## 64 0.0631980623
## 65 0.2387063266
## 66 0.0047317991
## 67 1.0000000000
## 68 0.5413034164
## 69 0.0447084452
## 70 0.2676088827
## 71 0.4334044691
## 72 0.0391657633
## 73 1.0000000000
## 74 0.4121089950
## 75 0.2671710214
## 76 1.0000000000
## 77 0.0094732333
## 78 1.0000000000
## 79 0.9275701361
## 80 0.3324687347
## 81 0.0044926275
## 82 0.0162484649
## 83 0.1070026247
## 84 0.0204581929
## 85 0.1234005721
## 86 0.3935677605
## 87 0.0424183386
## 88 1.0000000000
## 89 1.0000000000
## 90 1.0000000000
## 91 0.4901871882
## 92 1.0000000000
## 93 0.2713246035
## 94 0.6975431036
## 95 0.3658028354
## 96 0.0046196980
## 97 0.1261249260
## 98 0.0024012824
## 99 0.1326218392
## 100 0.3794934127
## 101 0.0012564392
## 102 0.3586670090
## 103 0.0102821675
## 104 0.0082160337
## 105 0.2412788996
## 106 0.3767102775
## 107 1.0000000000
## 108 1.0000000000
## 109 0.3187823160
## 110 0.2137070806
## 111 0.4853168412
## 112 0.1388934736
## 113 0.1034902775
## 114 0.0558762073
## 115 0.0820375496
## 116 0.6694202121
## 117 0.8826423306
## 118 0.2614213803
## 119 0.4904227708
## 120 0.6875028854
## 121 0.8835776929
## 122 1.0000000000
## 123 0.0803408894
## 124 0.7517842324
## 125 0.9167360152
## 126 0.4857198005
## 127 0.7452721403
## 128 0.7149027621
## 129 0.1620472648
## 130 0.2966575199
## 131 0.2480272764
## 132 0.1299673636
## 133 0.0111437756
## 134 0.0164824923
## 135 0.2387063266
## 136 0.0250384492
## 137 0.0256800896
## 138 1.0000000000
## 139 0.6480271386
## 140 0.7288878198
## 141 1.0000000000
## 142 0.7957053668
## 143 0.2594510374
## 144 1.0000000000
## 145 1.0000000000
## 146 0.7267345380
## 147 0.7948028036
## 148 0.0033935021
## 149 0.3137767370
## 150 0.3999446988
## 151 0.0221216622
## 152 0.3980826609
## 153 1.0000000000
## 154 0.1247992388
## 155 0.5883071019
## 156 0.9224239331
## 157 0.0040859793
## 158 0.0080747600
## 159 0.0217140598
## 160 0.1039572843
## 161 0.5828178487
## 162 0.3575087190
## 163 0.0164881563
## 164 0.2568457024
## 165 0.4618480113
## 166 0.0156294863
## 167 0.0392880415
## 168 0.6054411249
## 169 0.2103234386
## 170 0.0030391116
## 171 0.9464485335
## 172 0.0265193144
## 173 0.6809636743
## 174 0.2547231745
## 175 0.2847862832
## 176 0.6080993973
## 177 0.8389101085
## 178 0.6239682822
## 179 0.9863917980
## 180 0.6561035392
## 181 1.0000000000
## 182 0.3830449019
## 183 0.0135854904
## 184 0.2619882122
## 185 0.0153559032
## 186 0.0542553613
## 187 0.2387063266
## 188 0.0072146190
## 189 0.6445461335
## 190 0.0085203735
## 191 1.0000000000
## 192 0.0007766992
## 193 0.1305281065
## 194 0.4469540639
## 195 0.2417277227
## 196 0.0059081539
## 197 0.4598882088
## 198 0.4974841771
## 199 1.0000000000
## 200 0.6287260829
## 201 0.0246465740
## 202 0.2032340829
## 203 0.4300056455
## 204 0.0584705193
## 205 0.4106355889
## 206 0.0356193934
## 207 0.0214939042
## 208 0.6943789163
## 209 0.2593878772
## 210 0.8039092163
## 211 0.1060463785
## 212 1.0000000000
## 213 0.0277624728
## 214 0.7133425905
## 215 0.3129224078
## 216 0.1886814275
## 217 0.4285575619
## 218 0.0173039763
## 219 0.5326491365
## 220 0.5354549968
## 221 0.0408641707
## 222 0.1685800248
## 223 0.7487910112
## 224 0.7769198177
## 225 0.2278523568
## 226 0.9325646033
## 227 0.0427852402
## 228 0.8808429823
## 229 0.0109124983
## 230 0.9973410612
## 231 0.7339011375
## 232 0.7139655556
## 233 0.3989601298
## 234 1.0000000000
## 235 0.4009539803
## 236 0.7947279933
## 237 0.3454561771
## 238 1.0000000000
## 239 0.2387063266
## 240 1.0000000000
## 241 0.1184087562
## 242 1.0000000000
## 243 0.0629626136
## 244 0.9044840102
## 245 1.0000000000
## 246 0.1748954459
## 247 1.0000000000
## 248 0.6457238375
## 249 0.0268561470
## 250 0.0976670854
## 251 0.2475094293
## 252 0.3360580106
## 253 0.0769635029
## 254 0.3840867967
## 255 0.2387063266
## 256 0.1371392138
## 257 0.1559376606
## 258 0.5574713238
## 259 0.6516841777
## 260 0.0566512431
## 261 0.2387063272
## 262 1.0000000000
## 263 0.0256809397
## 264 0.0009340067
## 265 0.1258046843
## 266 0.7700648305
## 267 1.0000000000
## 268 0.1219583356
## 269 0.0079596767
## 270 0.0251617532
## 271 0.0031543984
## 272 1.0000000000
## 273 0.7857957571
## 274 0.1074764853
## 275 0.5896214022
## 276 0.2387063266
## 277 0.1287117527
## 278 0.2440284839
## 279 0.5693658859
## 280 0.7570350121
## 281 0.0275940954
## 282 0.4837001033
## 283 0.0788350647
## 284 0.0016854662
## 285 0.3726410302
## 286 0.0378797386
## 287 0.0173153442
## 288 0.4675060542
## 289 1.0000000000
## 290 0.5485760509
## 291 0.1180557523
## 292 0.0644493011
## 293 0.6590343481
## 294 0.6997176131
## 295 0.0518864394
## 296 0.0036781233
## 297 0.0589770250
## 298 0.0245770666
## 299 0.2606307412
## 300 0.2634805331
## 301 0.9865020155
## 302 0.9747448835
## 303 0.1216636414
## 304 0.1046183723
## 305 0.0174675738
## 306 0.0358305705
## 307 0.5790972428
## 308 1.0000000000
## 309 0.5287049263
## 310 0.0961013186
## 311 0.2387063277
## 312 1.0000000000
## 313 0.2592314951
## 314 0.3085965215
## 315 0.6179657320
## 316 0.0022848286
## 317 0.3253021431
## 318 0.1094582567
## 319 0.9700200727
## 320 0.0105667494
## 321 0.4106422400
## 322 0.3116400508
## 323 0.2312492234
## 324 0.0258446175
## 325 0.8610790285
## 326 0.2387063266
## 327 0.7244238134
## 328 0.0212495571
## 329 0.8962675296
## 330 0.4191797755
## 331 0.0015199879
## 332 0.0251159423
## 333 0.0021680700
## 334 1.0000000000
## 335 0.0056471447
## 336 0.0010077043
## 337 0.1803450124
## 338 0.5913430066
## 339 1.0000000000
## 340 0.9969297217
## 341 1.0000000000
## 342 1.0000000000
## 343 0.6627176203
## 344 0.7612896937
## 345 0.0414154176
## 346 0.2358971382
## 347 0.9716313323
## 348 1.0000000000
## 349 0.3657579124
## 350 0.2898954730
## 351 0.0390686948
## 352 0.5237499587
## 353 0.0030010651
## 354 0.5559665608
## 355 0.1978761588
## 356 0.6877624448
## 357 0.0487382350
## 358 0.0320943899
## 359 1.0000000000
## 360 0.0324369260
## 361 0.7936106721
## 362 0.2055781901
## 363 0.0092790325
## 364 0.4067066355
## 365 0.3213343320
## 366 0.1122794624
##
## $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 1.059354 13.68486 0.64752416 0.42102538 0.7190866 1
## 2 -2.377079 13.42732 3.08234940 0.07918794 0.3116429 2
## 3 -0.392660 13.60684 0.09235521 0.76121271 0.9835711 3
## 4 -2.120548 13.50604 2.46639853 0.11634736 0.3801544 4
## 5 -2.709153 13.58856 3.81911258 0.05070909 0.2410328 5
## 6 -1.530199 13.68581 1.21236993 0.27089947 0.5707173 6
## SpatialFDR contrast PValue_adj_withinNhood
## 1 0.7360658 Age1wk - Age4wk 0.8420508
## 2 0.3094980 Age1wk - Age4wk 0.3167518
## 3 0.9945429 Age1wk - Age4wk 0.7612127
## 4 0.3762469 Age1wk - Age4wk 0.1653436
## 5 0.2409513 Age1wk - Age4wk 0.2028364
## 6 0.5831511 Age1wk - Age4wk 0.634408722.4 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)22.5 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)