library(DSS)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

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    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: bsseq
Loading required package: GenomicRanges
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library(bsseq)
library(dplyr)

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library(kableExtra)

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library(ggplot2)
library(knitr)

Preprocessing

# read in sample names
samples <- read.table(file="../scripts/allsamples.txt", sep="\t", header=F, stringsAsFactors=F)$V1

# read in methylation data in tab delimited format: <chromosome> <position> <count total> <count methylated>
dat.list <- vector(mode = "list", length = length(samples))

for (i in 1:length(samples)){
        dat.list[[i]] <- read.table(paste0("../04-Methylation/", samples[i], ".CpG.counts.txt"), header=F, col.names=c("chr", "pos", "N", "X"))
}


# save BSseqData for future easy loading
BSobj <- makeBSseqData(dat.list, samples)
save(BSobj, file="BSobj.RData")
#load("BSobj.RData")


The original data included 1418084 CpG sites across all samples.

# remove the CpG sites on un-placed contigs
chr.use <- paste0("chr", c(1:22, "M", "X", "Y"))
dat <- chrSelectBSseq(BSobj, seqnames= chr.use, order=T)


CpG sites from unplaced contigs were removed, leaving 1418084 CpG sites.

Multidimensional scaling (MDS) plot of raw methylation data.

# create meta data for samples
stage <- c(rep("3M", 3), rep("24M", 3))
pdata <- data.frame(Samples=samples, EM.stage=stage, stringsAsFactors=F)
pdata$EM.stage <- factor(pdata$EM.stage, levels=c("3M", "24M"))
idx <- match(samples, pdata$Samples)
pdata <- pdata[idx,]

# set plot point type for the two groups
pchs <- ifelse(pdata$EM.stage == "3M", 15, 16)
# MDS plot
pct.meth <- getMeth(dat, type = "raw")
limma::plotMDS(asin(pct.meth), col = "blue", pch = pchs)
legend("bottomright", title = "EM.stage", legend = levels(pdata$EM.stage), pch = unique(pchs), text.font = 0.8)


Differential methylation analyses

Differential methylation analyses were conducted in DSS bioconductor package.


Comparison EM.24M vs EM.3M

Wald test was used.

Output files include the following:

  • mu1, mu2: group means

  • diff, diff.se: differece between group means and the standard error of differences

  • stat: hypothesis test statistics (Wald test)

  • phi1, phi2: dispersions

  • pvals: Raw p-value from test that the methylation difference differs from 0

  • fdrs: Benjamini-Hochberg false discovery rate (FDR) adjusted p-value


# differential methylation 24M vs 3M test (Wald test)
dmlTest <- DMLtest(BSobj, group1=samples[1:3], group2=samples[4:6], smoothing=TRUE)
Smoothing ...
Estimating dispersion for each CpG site, this will take a while ...

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Computing test statistics ...
# save test result for future easy loading
save(dmlTest, file="DML.RData")
# loading previously saved test results
#load("DML.RData")

#
# call differentially methylated CpG sites
dmls <- callDML(dmlTest, p.threshold=1.0)
# write DML results to file
write.table(dmls, file="Differential_methylation_CpG_24Mvs3M.txt", sep="\t", col.names=T, row.names=F, quote=F)


# list the top 500 differentially methylated CpG sites (ordered by P values)
n <- ncol(dmls)
header1 <- n
names(header1) <- paste0("Number of differentially methylated CpGs with FDR adjusted P < 0.05 = ", length(which(dmls$fdr < 0.05)))
header2 <- n
names(header2) <- "Top 500 CpG sites"
kable(dmls[1:500,], align = 'c', row.names=F) %>%
  add_header_above(header1, align = 'l') %>%
  add_header_above(header2, font_size = "larger", bold = T, align = "l") %>%
  kable_styling(bootstrap_options = c("hover", "condensed", "responsive"), full_width = T) %>%
  scroll_box(height = "500px")
Top 500 CpG sites
Number of differentially methylated CpGs with FDR adjusted P < 0.05 = 137
chr pos mu1 mu2 diff diff.se stat phi1 phi2 pval fdr postprob.overThreshold
chr18 27705890 0.1359743 0.5992355 -0.4632612 0.0570730 -8.116999 0.0454689 0.0295088 0.0000000 0.0000000 1.0000000
chr18 76788275 0.3031786 0.9576704 -0.6544918 0.0887605 -7.373682 0.0415192 0.0265846 0.0000000 0.0000000 1.0000000
chr18 76788286 0.3031786 0.9576704 -0.6544918 0.1106945 -5.912596 0.0415192 0.0265846 0.0000000 0.0002041 0.9999997
chr18 50961156 0.6125266 0.9724943 -0.3599677 0.0549520 -6.550586 0.0415192 0.0266366 0.0000000 0.0000080 0.9999989
chr18 44292096 0.7404710 0.9793312 -0.2388602 0.0293626 -8.134852 0.0415192 0.0265846 0.0000000 0.0000000 0.9999989
chr18 70108477 0.8861006 0.5387680 0.3473326 0.0532635 6.521027 0.0415192 0.0265846 0.0000000 0.0000088 0.9999983
chr18 6745843 0.8882682 0.4724788 0.4157894 0.0682040 6.096263 0.0415192 0.0265846 0.0000000 0.0000797 0.9999982
chr18 58546537 0.8069866 0.4685227 0.3384639 0.0516097 6.558142 0.0415192 0.0265846 0.0000000 0.0000080 0.9999981
chr18 20129923 0.9828184 0.5034878 0.4793306 0.0822035 5.831024 0.0419663 0.0237288 0.0000000 0.0003071 0.9999980
chr18 3999770 0.9749734 0.5588323 0.4161411 0.0715029 5.819915 0.0415192 0.0265846 0.0000000 0.0003156 0.9999951
chr18 6275295 0.4570788 0.8741066 -0.4170278 0.0719800 -5.793661 0.0415192 0.0265846 0.0000000 0.0003555 0.9999947
chr18 4184336 0.2399108 0.6033839 -0.3634731 0.0600421 -6.053640 0.0415192 0.0265846 0.0000000 0.0000987 0.9999943
chr18 26619315 0.1445599 0.5849468 -0.4403870 0.0776969 -5.668014 0.0464096 0.0260469 0.0000000 0.0005753 0.9999941
chr18 79180964 0.8933565 0.5461697 0.3471868 0.0575781 6.029844 0.0415192 0.0265846 0.0000000 0.0001089 0.9999912
chr18 4897829 0.7851835 0.3603503 0.4248332 0.0758113 5.603824 0.0415192 0.0265846 0.0000000 0.0007494 0.9999909
chr18 88339401 0.9882562 0.6061936 0.3820626 0.0680518 5.614290 0.0422176 0.0650805 0.0000000 0.0007240 0.9999830
chr18 3236960 0.6936342 0.9863807 -0.2927465 0.0471871 -6.203957 0.0384476 0.0269248 0.0000000 0.0000451 0.9999779
chr18 26499595 0.9004923 0.5984799 0.3020125 0.0495162 6.099263 0.0415192 0.0265846 0.0000000 0.0000797 0.9999775
chr18 88339402 0.9882562 0.6061936 0.3820626 0.0699310 5.463420 0.0425735 0.0460826 0.0000000 0.0012671 0.9999725
chr18 3941121 0.7638484 0.9781954 -0.2143469 0.0285076 -7.518946 0.0415192 0.0265846 0.0000000 0.0000000 0.9999698
chr18 41447117 0.9355798 0.6914643 0.2441155 0.0361056 6.761155 0.0415192 0.0265846 0.0000000 0.0000027 0.9999672
chr18 7987276 0.5680178 0.1379195 0.4300983 0.0831024 5.175521 0.0366147 0.0242206 0.0000002 0.0050283 0.9999644
chr18 32885208 0.4920893 0.8385519 -0.3464627 0.0622052 -5.569678 0.0415192 0.0265846 0.0000000 0.0008676 0.9999629
chr18 17178540 0.6580969 0.9669160 -0.3088191 0.0537681 -5.743539 0.0415192 0.0265846 0.0000000 0.0004456 0.9999486
chr18 52050734 0.8637562 0.5120838 0.3516725 0.0651998 5.393769 0.0415192 0.0265846 0.0000001 0.0018071 0.9999433
chr18 20129922 0.9828184 0.5034878 0.4793306 0.0988049 4.851286 0.0424017 0.0280688 0.0000012 0.0178097 0.9999383
chr18 15652492 0.9448666 0.7554247 0.1894418 0.0234593 8.075351 0.0415192 0.0265846 0.0000000 0.0000000 0.9999313
chr18 10429512 0.4397118 0.8296125 -0.3899007 0.0762119 -5.116005 0.0415192 0.0269402 0.0000003 0.0060452 0.9999288
chr18 71966059 0.9134439 0.5994790 0.3139649 0.0562960 5.577041 0.0415192 0.0249688 0.0000000 0.0008525 0.9999279
chr18 42284660 0.7565171 0.3721742 0.3843429 0.0751273 5.115887 0.0354818 0.0237543 0.0000003 0.0060452 0.9999231
chr18 85448173 0.9728425 0.5493923 0.4234502 0.0854933 4.953022 0.0419311 0.0252422 0.0000007 0.0123902 0.9999226
chr18 43406349 0.8018325 0.5624849 0.2393476 0.0376616 6.355216 0.0415192 0.0265846 0.0000000 0.0000186 0.9998922
chr18 14379317 0.5713505 0.8773970 -0.3060465 0.0558574 -5.479070 0.0415192 0.0265846 0.0000000 0.0011919 0.9998873
chr18 49811791 0.7033488 0.9152131 -0.2118644 0.0303522 -6.980205 0.0415192 0.0265846 0.0000000 0.0000007 0.9998859
chr18 37381665 0.7933874 0.3620615 0.4313259 0.0899469 4.795338 0.0347356 0.0228079 0.0000016 0.0221922 0.9998850
chr18 71483695 0.5810713 0.9535608 -0.3724896 0.0746322 -4.991004 0.0402160 0.0288120 0.0000006 0.0104654 0.9998694
chr18 48548491 0.9842397 0.6903757 0.2938640 0.0532758 5.515903 0.0416337 0.0268697 0.0000000 0.0010933 0.9998631
chr18 18480278 0.9764181 0.5821617 0.3942564 0.0811759 4.856819 0.0415801 0.0317455 0.0000012 0.0176879 0.9998555
chr18 60275148 0.9212132 0.5518046 0.3694085 0.0756316 4.884314 0.0415192 0.0289262 0.0000010 0.0162546 0.9998161
chr18 9829221 0.7945722 0.4509168 0.3436554 0.0688171 4.993751 0.0435908 0.0289113 0.0000006 0.0104481 0.9998004
chr18 89676668 0.9429154 0.6164613 0.3264540 0.0640528 5.096638 0.0415192 0.0265846 0.0000003 0.0065122 0.9997964
chr18 86660572 0.5066879 0.7734085 -0.2667206 0.0472849 -5.640712 0.0415192 0.0265846 0.0000000 0.0006380 0.9997890
chr18 33755271 0.6342991 0.9735533 -0.3392542 0.0682688 -4.969391 0.0415192 0.0265846 0.0000007 0.0115574 0.9997713
chr18 52895307 0.9800047 0.6523109 0.3276938 0.0652861 5.019353 0.0418297 0.0266478 0.0000005 0.0093850 0.9997563
chr18 73134688 0.3599157 0.7096348 -0.3497191 0.0717099 -4.876861 0.0415192 0.0265846 0.0000011 0.0165097 0.9997515
chr18 77994796 0.5450973 0.8373093 -0.2922120 0.0557638 -5.240170 0.0449213 0.0265846 0.0000002 0.0039230 0.9997165
chr18 66616018 0.8125584 0.4389725 0.3735859 0.0798641 4.677771 0.0488357 0.0248238 0.0000029 0.0342566 0.9996933
chr18 18480277 0.9764181 0.5821617 0.3942564 0.0859589 4.586568 0.0425286 0.0222314 0.0000045 0.0486359 0.9996906
chr18 10967246 0.4686354 0.8767019 -0.4080665 0.0905834 -4.504873 0.0440032 0.0273233 0.0000066 0.0629719 0.9996642
chr18 3205594 0.9709460 0.7101680 0.2607780 0.0473033 5.512892 0.0415192 0.0265846 0.0000000 0.0010933 0.9996617
chr18 90098340 0.6263634 0.9094402 -0.2830768 0.0538976 -5.252122 0.0415192 0.0265846 0.0000002 0.0038104 0.9996590
chr18 41592048 0.8129749 0.4631494 0.3498255 0.0737910 4.740758 0.0427871 0.0277121 0.0000021 0.0274792 0.9996449
chr18 51079163 0.2965761 0.6958993 -0.3993231 0.0885437 -4.509898 0.0413836 0.0224421 0.0000065 0.0626075 0.9996383
chr18 46315308 0.9820364 0.7008343 0.2812022 0.0536186 5.244491 0.0416167 0.0230912 0.0000002 0.0039006 0.9996369
chr18 87623436 0.5946804 0.9352656 -0.3405851 0.0719362 -4.734547 0.0393866 0.0266360 0.0000022 0.0280536 0.9995877
chr18 76788287 0.3031786 0.9576704 -0.6544918 0.1665195 -3.930420 0.0384168 0.0275475 0.0000848 0.3030617 0.9995685
chr18 89676609 0.9429154 0.6164613 0.3264540 0.0685775 4.760363 0.0416866 0.0265846 0.0000019 0.0254106 0.9995203
chr18 61467660 0.9421171 0.6711264 0.2709907 0.0521576 5.195609 0.0422029 0.0265846 0.0000002 0.0046625 0.9994779
chr18 37381666 0.7933874 0.3620615 0.4313259 0.1013182 4.257142 0.0306790 0.0208473 0.0000207 0.1329971 0.9994626
chr18 8814172 0.9397416 0.5893603 0.3503814 0.0768225 4.560924 0.0435901 0.0255877 0.0000051 0.0514398 0.9994414
chr18 33788097 0.9147396 0.4992388 0.4155007 0.0973381 4.268634 0.0417711 0.0265846 0.0000197 0.1281222 0.9994051
chr18 33788099 0.9147396 0.4992388 0.4155007 0.0973381 4.268634 0.0417711 0.0265846 0.0000197 0.1281222 0.9994051
chr18 88865298 0.7450399 0.9880315 -0.2429916 0.0441659 -5.501797 0.0360916 0.0269417 0.0000000 0.0011149 0.9993973
chr18 80205217 0.4990469 0.8488508 -0.3498039 0.0772385 -4.528883 0.0441498 0.0301098 0.0000059 0.0582038 0.9993901
chr18 24067280 0.7288889 0.5066694 0.2222195 0.0379929 5.848977 0.0415192 0.0265846 0.0000000 0.0002873 0.9993521
chr18 34092860 0.3636795 0.6892694 -0.3255899 0.0702411 -4.635322 0.0415192 0.0265846 0.0000036 0.0397391 0.9993401
chr18 71483694 0.5810713 0.9535608 -0.3724896 0.0848876 -4.388034 0.0423837 0.0202138 0.0000114 0.0916246 0.9993364
chr18 4426200 0.8328780 0.4708269 0.3620511 0.0821088 4.409409 0.0420621 0.0282472 0.0000104 0.0858812 0.9992924
chr18 7987275 0.5680178 0.1379195 0.4300983 0.1038430 4.141814 0.0343716 0.0298266 0.0000345 0.1752824 0.9992608
chr18 14184062 0.9536770 0.6486621 0.3050149 0.0645007 4.728861 0.0439552 0.0261835 0.0000023 0.0283518 0.9992598
chr18 54985324 0.6588352 0.9743579 -0.3155227 0.0678429 -4.650784 0.0415192 0.0265846 0.0000033 0.0380917 0.9992554
chr18 85498300 0.9333407 0.6403656 0.2929750 0.0607513 4.822531 0.0415192 0.0265846 0.0000014 0.0195618 0.9992546
chr18 29288186 0.9465243 0.6479676 0.2985567 0.0625564 4.772597 0.0426847 0.0230631 0.0000018 0.0241420 0.9992483
chr18 59986435 0.9191558 0.6964245 0.2227313 0.0389811 5.713823 0.0415192 0.0265846 0.0000000 0.0004812 0.9991794
chr18 3274893 0.6895518 0.9727220 -0.2831702 0.0583510 -4.852874 0.0415192 0.0265846 0.0000012 0.0178097 0.9991527
chr18 26915547 0.9261607 0.6427852 0.2833755 0.0585616 4.838928 0.0358505 0.0265846 0.0000013 0.0187581 0.9991299
chr18 39440899 0.8101954 0.4713326 0.3388628 0.0764860 4.430387 0.0356495 0.0290764 0.0000094 0.0823512 0.9991048
chr18 27705889 0.1359743 0.5992355 -0.4632612 0.1164741 -3.977377 0.0316748 0.0193844 0.0000697 0.2728157 0.9990928
chr18 72282562 0.8731957 0.5440641 0.3291316 0.0734796 4.479227 0.0722529 0.0249688 0.0000075 0.0691510 0.9990905
chr18 11137993 0.9396234 0.6449232 0.2947002 0.0624385 4.719850 0.0357553 0.0296920 0.0000024 0.0291125 0.9990904
chr18 6572038 0.6199008 0.9192658 -0.2993649 0.0641976 -4.663183 0.0334363 0.0256852 0.0000031 0.0364304 0.9990502
chr18 44946061 0.8991524 0.6719194 0.2272330 0.0412185 5.512894 0.0415192 0.0265846 0.0000000 0.0010933 0.9989884
chr18 86350490 0.9662702 0.7387057 0.2275645 0.0413510 5.503237 0.0415192 0.0265846 0.0000000 0.0011149 0.9989820
chr18 72044193 0.6732604 0.2751945 0.3980658 0.0966291 4.119523 0.0497032 0.0236148 0.0000380 0.1855471 0.9989811
chr18 35601494 0.6436401 0.9784833 -0.3348432 0.0768366 -4.357862 0.0461787 0.0268136 0.0000131 0.0991910 0.9988799
chr18 72169692 0.6268819 0.9366097 -0.3097278 0.0686921 -4.508929 0.0332414 0.0242311 0.0000065 0.0626075 0.9988678
chr18 54983529 0.8730148 0.4685687 0.4044461 0.0997300 4.055412 0.0417491 0.9894752 0.0000500 0.2235771 0.9988663
chr18 41352385 0.4928893 0.1652186 0.3276707 0.0749252 4.373304 0.0353647 0.0205810 0.0000122 0.0947655 0.9988118
chr18 4461122 0.7227184 0.9841079 -0.2613895 0.0532300 -4.910569 0.0430284 0.0270730 0.0000009 0.0145492 0.9987850
chr18 59394208 0.8843860 0.5200291 0.3643569 0.0872877 4.174205 0.0367941 0.0303132 0.0000299 0.1628116 0.9987715
chr18 39494763 0.7508195 0.9856358 -0.2348163 0.0448626 -5.234125 0.0383424 0.0266343 0.0000002 0.0039837 0.9986725
chr18 72470181 0.2636851 0.5536791 -0.2899940 0.0632559 -4.584461 0.0415192 0.0281403 0.0000046 0.0486359 0.9986659
chr18 22462692 0.9850087 0.7192352 0.2657735 0.0555549 4.783984 0.0417503 0.0265846 0.0000017 0.0230325 0.9985773
chr18 8636264 0.3086341 0.6582554 -0.3496213 0.0838932 -4.167459 0.0415192 0.0265846 0.0000308 0.1644911 0.9985373
chr18 79815488 0.9606927 0.7383977 0.2222950 0.0412334 5.391141 0.0421097 0.0241262 0.0000001 0.0018071 0.9984911
chr18 18693724 0.4695195 0.8035945 -0.3340749 0.0790047 -4.228543 0.0446631 0.0265846 0.0000235 0.1407056 0.9984757
chr18 51282073 0.6553955 0.3515626 0.3038329 0.0688641 4.412068 0.0390713 0.0238350 0.0000102 0.0858812 0.9984615
chr18 73444505 0.1190599 0.3349232 -0.2158633 0.0393250 -5.489216 0.0415192 0.0265846 0.0000000 0.0011484 0.9983920
chr18 29383221 0.9706798 0.7051067 0.2655730 0.0564038 4.708420 0.0415192 0.0265846 0.0000025 0.0305231 0.9983349
chr18 54849907 0.7626734 0.3836918 0.3789816 0.0958679 3.953164 0.0440284 0.0227863 0.0000771 0.2851439 0.9981935
chr18 26619314 0.1445599 0.5849468 -0.4403870 0.1169861 -3.764439 0.0426301 0.0357543 0.0001669 0.4598115 0.9981927
chr18 8965179 0.8158872 0.4413740 0.3745132 0.0946565 3.956548 0.0545744 0.0261612 0.0000760 0.2851439 0.9981350
chr18 17884478 0.9462472 0.6513858 0.2948615 0.0672198 4.386529 0.0411019 0.0247588 0.0000115 0.0917334 0.9981275
chr18 29011712 0.9736893 0.7690227 0.2046666 0.0361406 5.663067 0.0415192 0.0265846 0.0000000 0.0005757 0.9981108
chr18 56460416 0.7124685 0.9607878 -0.2483193 0.0514256 -4.828713 0.0517949 0.0269923 0.0000014 0.0191539 0.9980377
chr18 79602444 0.7093100 0.3677977 0.3415123 0.0838532 4.072737 0.0382452 0.0276370 0.0000465 0.2130363 0.9980128
chr18 87944360 0.7848684 0.5024538 0.2824146 0.0634596 4.450306 0.0415192 0.0249688 0.0000086 0.0761268 0.9979767
chr18 51079162 0.2965761 0.6958993 -0.3993231 0.1043105 -3.828216 0.0330685 0.0212454 0.0001291 0.4024837 0.9979455
chr18 90069436 0.9818616 0.6670851 0.3147765 0.0749035 4.202427 0.0416511 0.0257157 0.0000264 0.1515308 0.9979306
chr18 22627106 0.7133156 0.9799193 -0.2666037 0.0581936 -4.581323 0.0341155 0.0268005 0.0000046 0.0486359 0.9979012
chr18 20144815 0.2275428 0.6214426 -0.3938998 0.1031218 -3.819754 0.0368375 0.0263896 0.0001336 0.4082771 0.9978151
chr18 63615191 0.7036187 0.3798692 0.3237495 0.0785756 4.120229 0.0376622 0.0208463 0.0000378 0.1855471 0.9977973
chr18 39440898 0.8101954 0.4713326 0.3388628 0.0841177 4.028436 0.0300278 0.0318031 0.0000561 0.2393356 0.9977418
chr18 8331514 0.5959395 0.2739571 0.3219824 0.0784654 4.103496 0.0333082 0.0184431 0.0000407 0.1915699 0.9976657
chr18 85448172 0.9728425 0.5493923 0.4234502 0.1145311 3.697251 0.0421529 0.0268694 0.0002179 0.5473555 0.9976319
chr18 59394209 0.8843860 0.5200291 0.3643569 0.0937346 3.887112 0.0370843 0.0229110 0.0001014 0.3457133 0.9976012
chr18 22638440 0.9738574 0.5894693 0.3843882 0.1008620 3.811032 0.0419311 0.0248249 0.0001384 0.4121596 0.9975964
chr18 51034616 0.7783227 0.9764705 -0.1981479 0.0348805 -5.680760 0.0415192 0.0265846 0.0000000 0.0005497 0.9975522
chr18 70340883 0.9849617 0.7107520 0.2742097 0.0622014 4.408417 0.0416285 0.0273169 0.0000104 0.0858812 0.9974507
chr18 14594444 0.9072275 0.5778898 0.3293377 0.0821570 4.008636 0.0364983 0.0207116 0.0000611 0.2531474 0.9973765
chr18 82292682 0.6840182 0.9582598 -0.2742416 0.0624655 -4.390287 0.0415192 0.0265846 0.0000113 0.0912049 0.9973597
chr18 31248397 0.3675608 0.7427996 -0.3752388 0.0988341 -3.796653 0.0369330 0.0284721 0.0001467 0.4267736 0.9973232
chr18 22102017 0.9025752 0.5668629 0.3357122 0.0847738 3.960095 0.0415192 0.0265846 0.0000749 0.2851439 0.9972863
chr18 64629232 0.8479808 0.6207903 0.2271905 0.0458865 4.951138 0.0390249 0.0265846 0.0000007 0.0123902 0.9972130
chr18 36879860 0.7989477 0.5055561 0.2933916 0.0698163 4.202334 0.0508727 0.0248133 0.0000264 0.1515308 0.9971972
chr18 51221363 0.9693148 0.6901257 0.2791892 0.0647235 4.313565 0.0415192 0.0265846 0.0000161 0.1138851 0.9971845
chr18 10216799 0.5380076 0.9020787 -0.3640711 0.0954099 -3.815861 0.0417817 0.0243590 0.0001357 0.4092836 0.9971784
chr18 19187419 0.9021288 0.5933538 0.3087750 0.0756540 4.081409 0.0477153 0.0237557 0.0000448 0.2059183 0.9971064
chr18 42284659 0.7565171 0.3721742 0.3843429 0.1033414 3.719156 0.0308386 0.0218748 0.0001999 0.5227274 0.9970351
chr18 14594443 0.9072275 0.5778898 0.3293377 0.0835125 3.943574 0.0375707 0.0241188 0.0000803 0.2921460 0.9969852
chr18 87623435 0.5946804 0.9352656 -0.3405851 0.0877635 -3.880715 0.0309118 0.0279377 0.0001041 0.3506469 0.9969403
chr18 8285870 0.8175818 0.4998637 0.3177181 0.0795484 3.994023 0.0415192 0.0285179 0.0000650 0.2594437 0.9968993
chr18 10052104 0.7327747 0.4656410 0.2671338 0.0610775 4.373686 0.0380673 0.0249688 0.0000122 0.0947655 0.9968944
chr18 10052100 0.7327747 0.4656410 0.2671338 0.0610787 4.373599 0.0355117 0.0282170 0.0000122 0.0947655 0.9968939
chr18 62858779 0.9817661 0.7251615 0.2566046 0.0572731 4.480373 0.0421342 0.0284870 0.0000075 0.0691510 0.9968748
chr18 3670143 0.3060502 0.6513275 -0.3452773 0.0898504 -3.842802 0.0354165 0.0213125 0.0001216 0.3903282 0.9968321
chr18 69776641 0.7525882 0.9768325 -0.2242444 0.0455833 -4.919443 0.0511767 0.0265846 0.0000009 0.0140665 0.9967913
chr18 88515050 0.9847817 0.7248503 0.2599314 0.0587914 4.421245 0.0415981 0.0272522 0.0000098 0.0834807 0.9967390
chr18 15728999 0.7069291 0.9183028 -0.2113737 0.0409769 -5.158363 0.0415192 0.0283623 0.0000002 0.0051826 0.9967157
chr18 8915110 0.7843213 0.5594167 0.2249046 0.0459948 4.889786 0.0415192 0.0265846 0.0000010 0.0159889 0.9966925
chr18 3202301 0.4335815 0.8082433 -0.3746618 0.1013693 -3.696008 0.0451046 0.0219466 0.0002190 0.5481909 0.9966323
chr18 3202302 0.4335815 0.8082433 -0.3746618 0.1014793 -3.692004 0.0385008 0.0306967 0.0002225 0.5547785 0.9966024
chr18 35567555 0.7626270 0.9348853 -0.1722583 0.0267018 -6.451197 0.0415192 0.0265846 0.0000000 0.0000129 0.9965963
chr18 29293110 0.8556365 0.5110440 0.3445925 0.0904817 3.808421 0.0419818 0.0236148 0.0001399 0.4156467 0.9965669
chr18 67185955 0.9220283 0.6780946 0.2439338 0.0532457 4.581282 0.0397270 0.0265846 0.0000046 0.0486359 0.9965662
chr18 51376197 0.9889372 0.7249662 0.2639709 0.0606733 4.350695 0.0429757 0.0319608 0.0000136 0.1016954 0.9965592
chr18 59841553 0.9709460 0.6649684 0.3059776 0.0763494 4.007596 0.0415192 0.0243227 0.0000613 0.2531474 0.9965104
chr18 52998735 0.5901082 0.9234123 -0.3333041 0.0868360 -3.838318 0.0407498 0.0274143 0.0001239 0.3940112 0.9963924
chr18 7803010 0.6931439 0.9597383 -0.2665943 0.0620637 -4.295493 0.0415192 0.0265846 0.0000174 0.1179388 0.9963653
chr18 85412027 0.9367115 0.6638569 0.2728546 0.0645457 4.227309 0.0426715 0.0255420 0.0000237 0.1408744 0.9962971
chr18 17786157 0.7602678 0.9527978 -0.1925301 0.0346328 -5.559189 0.0415192 0.0265846 0.0000000 0.0008995 0.9962272
chr18 33788006 0.9147396 0.4992388 0.4155007 0.1182925 3.512486 0.0422440 0.0265846 0.0004439 0.8272376 0.9961814
chr18 63482434 0.9030487 0.6129989 0.2900498 0.0717040 4.045101 0.0382897 0.0258520 0.0000523 0.2278085 0.9959811
chr18 73692036 0.9451192 0.4325410 0.5125783 0.1558781 3.288328 0.0415192 0.0249688 0.0010078 0.9999991 0.9959796
chr18 73692051 0.9451192 0.4325410 0.5125783 0.1559275 3.287287 0.0415192 0.0280145 0.0010116 0.9999991 0.9959698
chr18 65930744 0.5382777 0.2871105 0.2511672 0.0570548 4.402209 0.0415192 0.0265846 0.0000107 0.0878565 0.9959695
chr18 61321824 0.9421764 0.6362593 0.3059171 0.0778257 3.930800 0.0437148 0.0265846 0.0000847 0.3030617 0.9959261
chr18 90133658 0.9219964 0.6362605 0.2857358 0.0702078 4.069861 0.0375451 0.0181373 0.0000470 0.2149763 0.9959217
chr18 52517228 0.4970581 0.8064482 -0.3093902 0.0791967 -3.906606 0.0693750 0.0229465 0.0000936 0.3253511 0.9959026
chr18 22638439 0.9738574 0.5894693 0.3843882 0.1076870 3.569495 0.0417351 0.0229477 0.0003577 0.7374780 0.9958688
chr18 10052050 0.7564003 0.4771996 0.2792006 0.0678696 4.113783 0.0419064 0.0370396 0.0000389 0.1883234 0.9958592
chr18 24060026 0.8756257 0.6338014 0.2418243 0.0538052 4.494440 0.0415192 0.0265846 0.0000070 0.0652517 0.9958041
chr18 10052099 0.7327747 0.4656410 0.2671338 0.0634866 4.207717 0.0504884 0.0308046 0.0000258 0.1504435 0.9957631
chr18 85865147 0.4486464 0.7812474 -0.3326010 0.0887191 -3.748924 0.0420595 0.0223678 0.0001776 0.4778739 0.9956268
chr18 18010044 0.5305020 0.8481402 -0.3176382 0.0833038 -3.813010 0.0463314 0.0234995 0.0001373 0.4115102 0.9955072
chr18 26028885 0.8337710 0.4589697 0.3748013 0.1061090 3.532230 0.0350516 0.0265846 0.0004121 0.8123910 0.9952023
chr18 10052221 0.6371979 0.3869461 0.2502518 0.0581590 4.302890 0.0415192 0.0265846 0.0000169 0.1161540 0.9951093
chr18 10052074 0.7403147 0.4704809 0.2698338 0.0657437 4.104330 0.0356412 0.0423386 0.0000405 0.1915699 0.9951066
chr18 40714756 0.4390751 0.8278898 -0.3888147 0.1119321 -3.473666 0.0380361 0.0241872 0.0005134 0.8780332 0.9950701
chr18 43423206 0.9204154 0.6061048 0.3143106 0.0830654 3.783895 0.0440272 0.0319787 0.0001544 0.4373853 0.9950606
chr18 8481767 0.7234858 0.9826656 -0.2591798 0.0617156 -4.199586 0.0413833 0.0269411 0.0000267 0.1521298 0.9950492
chr18 10052144 0.7279823 0.4710140 0.2569683 0.0609961 4.212867 0.0415192 0.0249688 0.0000252 0.1488150 0.9949650
chr18 10052149 0.7279823 0.4710140 0.2569683 0.0609961 4.212867 0.0415192 0.0249688 0.0000252 0.1488150 0.9949650
chr18 10052103 0.7327747 0.4656410 0.2671338 0.0650030 4.109558 0.0399561 0.0297370 0.0000396 0.1898341 0.9949322
chr18 17907723 0.9738741 0.6614956 0.3123785 0.0826314 3.780384 0.0415192 0.0265846 0.0001566 0.4402395 0.9949182
chr18 85814206 0.8936719 0.6879358 0.2057362 0.0411601 4.998443 0.0415192 0.0265846 0.0000006 0.0103278 0.9948989
chr18 23066200 0.2394678 0.5794266 -0.3399588 0.0934686 -3.637145 0.0453596 0.0249102 0.0002757 0.6330298 0.9948761
chr18 10051989 0.7566729 0.4786114 0.2780615 0.0693831 4.007624 0.0393010 0.0286368 0.0000613 0.2531474 0.9948613
chr18 85077515 0.9686480 0.7243753 0.2442727 0.0563353 4.336050 0.0415192 0.0265846 0.0000145 0.1064205 0.9947809
chr18 33768529 0.9490765 0.6679561 0.2811203 0.0709676 3.961247 0.0329722 0.0240894 0.0000746 0.2851439 0.9946471
chr18 62698279 0.5904027 0.9512146 -0.3608118 0.1022596 -3.528389 0.0339402 0.0266784 0.0004181 0.8133174 0.9946247
chr18 51667413 0.6849978 0.9286454 -0.2436477 0.0563554 -4.323415 0.0390249 0.0267223 0.0000154 0.1103809 0.9945978
chr18 10052206 0.6371979 0.3869461 0.2502518 0.0590864 4.235355 0.0415192 0.0277433 0.0000228 0.1388131 0.9945034
chr18 10052177 0.6678399 0.4112901 0.2565497 0.0615919 4.165319 0.0415192 0.0278752 0.0000311 0.1654077 0.9944847
chr18 9617108 0.8484580 0.5729463 0.2755117 0.0690559 3.989690 0.0537413 0.0181404 0.0000662 0.2634740 0.9944825
chr18 10052013 0.7564003 0.4771996 0.2792006 0.0705372 3.958203 0.0408236 0.0281653 0.0000755 0.2851439 0.9944655
chr18 90338779 0.4796450 0.8032306 -0.3235856 0.0880584 -3.674670 0.0354419 0.0215772 0.0002382 0.5763071 0.9944432
chr18 7599628 0.9446094 0.7028276 0.2417818 0.0558558 4.328677 0.0359331 0.0240040 0.0000150 0.1088993 0.9944312
chr18 10052139 0.7279823 0.4710140 0.2569683 0.0618499 4.154711 0.0415192 0.0248401 0.0000326 0.1706662 0.9944239
chr18 20144814 0.2275428 0.6214426 -0.3938998 0.1158552 -3.399932 0.0353472 0.0266302 0.0006740 0.9999991 0.9944163
chr18 10052172 0.6863975 0.4321308 0.2542667 0.0608561 4.178163 0.0415192 0.0279998 0.0000294 0.1612646 0.9943767
chr18 3441115 0.6202424 0.8750680 -0.2548256 0.0611125 -4.169780 0.0313167 0.0245764 0.0000305 0.1634514 0.9943528
chr18 43086637 0.4163586 0.7157860 -0.2994274 0.0787291 -3.803261 0.0467283 0.0238907 0.0001428 0.4208154 0.9943470
chr18 90133659 0.9219964 0.6362605 0.2857358 0.0736182 3.881322 0.0374288 0.0194441 0.0001039 0.3506203 0.9941815
chr18 10052116 0.7279823 0.4710140 0.2569683 0.0622732 4.126465 0.0390523 0.0248401 0.0000368 0.1833805 0.9941429
chr18 52517227 0.4970581 0.8064482 -0.3093902 0.0830914 -3.723493 0.0384074 0.0187918 0.0001965 0.5167342 0.9941327
chr18 40714755 0.4390751 0.8278898 -0.3888147 0.1146751 -3.390575 0.0447521 0.0288675 0.0006975 0.9999991 0.9941181
chr18 90041206 0.1805662 0.5061890 -0.3256228 0.0896074 -3.633882 0.0431780 0.0249275 0.0002792 0.6379399 0.9940982
chr18 10052135 0.7279823 0.4710140 0.2569683 0.0623827 4.119221 0.0415192 0.0248401 0.0000380 0.1855471 0.9940688
chr18 8331513 0.5959395 0.2739571 0.3219824 0.0883188 3.645682 0.0299910 0.0197204 0.0002667 0.6200831 0.9940226
chr18 19187420 0.9021288 0.5933538 0.3087750 0.0831199 3.714814 0.0445726 0.0206193 0.0002034 0.5268429 0.9939934
chr18 68364829 0.9336776 0.6362128 0.2974648 0.0786238 3.783396 0.0351931 0.0215377 0.0001547 0.4373853 0.9939895
chr18 3358343 0.9850959 0.6992617 0.2858341 0.0742330 3.850497 0.0425878 0.0216385 0.0001179 0.3821005 0.9938496
chr18 83697833 0.8853226 0.5805762 0.3047464 0.0818016 3.725435 0.0422421 0.0201486 0.0001950 0.5137406 0.9938425
chr18 33768528 0.9490765 0.6679561 0.2811203 0.0723810 3.883897 0.0425705 0.0213771 0.0001028 0.3490797 0.9938309
chr18 9438090 0.9359379 0.7766550 0.1592829 0.0237192 6.715359 0.0415192 0.0265846 0.0000000 0.0000033 0.9937792
chr18 14397495 0.7668246 0.9717626 -0.2049380 0.0419957 -4.879982 0.0415192 0.0265846 0.0000011 0.0164311 0.9937690
chr18 18781316 0.7348971 0.9808761 -0.2459790 0.0584457 -4.208673 0.0341486 0.0267888 0.0000257 0.1504376 0.9937496
chr18 89134557 0.9864468 0.7382886 0.2481582 0.0593196 4.183412 0.0424214 0.0213630 0.0000287 0.1588351 0.9937486
chr18 52895306 0.9800047 0.6523109 0.3276938 0.0912062 3.592889 0.0424797 0.0207145 0.0003270 0.6980552 0.9937296
chr18 72169693 0.6268819 0.9366097 -0.3097278 0.0840202 -3.686347 0.0457618 0.0288339 0.0002275 0.5612256 0.9937232
chr18 10052125 0.7279823 0.4710140 0.2569683 0.0629127 4.084525 0.0425065 0.0248401 0.0000442 0.2038469 0.9937025
chr18 3670142 0.3060502 0.6513275 -0.3452773 0.0983372 -3.511155 0.0479941 0.0214941 0.0004462 0.8288784 0.9936917
chr18 20133750 0.9898095 0.7171429 0.2726666 0.0692480 3.937540 0.0423330 0.2036026 0.0000823 0.2972600 0.9936747
chr18 3131496 0.7612499 0.9838771 -0.2226271 0.0492176 -4.523321 0.0423866 0.0268314 0.0000061 0.0593373 0.9936403
chr18 27029408 0.9718312 0.7044817 0.2673495 0.0672081 3.977938 0.0415192 0.0316702 0.0000695 0.2728157 0.9936133
chr18 24787917 0.4289203 0.1548270 0.2740933 0.0699834 3.916546 0.0365223 0.0265846 0.0000898 0.3177759 0.9935703
chr18 52198885 0.7874982 0.5003396 0.2871587 0.0753280 3.812110 0.0387835 0.0284957 0.0001378 0.4121258 0.9935150
chr18 89544067 0.9380497 0.4944328 0.4436169 0.1388525 3.194878 0.0355764 0.0277403 0.0013989 0.9999991 0.9933776
chr18 37527276 0.6361135 0.8799111 -0.2437975 0.0580512 -4.199696 0.0415192 0.0265846 0.0000267 0.1521298 0.9933769
chr18 10051981 0.7713326 0.5076365 0.2636961 0.0661060 3.988991 0.0321884 0.0248324 0.0000664 0.2634987 0.9933618
chr18 10052148 0.7279823 0.4710140 0.2569683 0.0634459 4.050194 0.0498529 0.0248401 0.0000512 0.2253554 0.9933204
chr18 10052134 0.7279823 0.4710140 0.2569683 0.0634471 4.050117 0.0390249 0.0323713 0.0000512 0.2253554 0.9933196
chr18 10052138 0.7279823 0.4710140 0.2569683 0.0634471 4.050117 0.0390249 0.0323713 0.0000512 0.2253554 0.9933196
chr18 10052143 0.7279823 0.4710140 0.2569683 0.0634515 4.049841 0.0425065 0.0323713 0.0000513 0.2253554 0.9933164
chr18 27942200 0.9718312 0.6594683 0.3123629 0.0859051 3.636137 0.0415192 0.0305460 0.0002768 0.6344650 0.9932840
chr18 32993960 0.5542468 0.9088841 -0.3546373 0.1031161 -3.439205 0.0409582 0.0276059 0.0005834 0.9455829 0.9932387
chr18 49620049 0.6648600 0.9261426 -0.2612825 0.0653216 -3.999940 0.0340056 0.0238658 0.0000634 0.2567198 0.9932265
chr18 41819191 0.7334878 0.4230172 0.3104705 0.0854319 3.634129 0.0322257 0.0250376 0.0002789 0.6379399 0.9931234
chr18 66616017 0.8125584 0.4389725 0.3735859 0.1113430 3.355272 0.0424020 0.0207831 0.0007929 0.9999991 0.9930082
chr18 3236959 0.6936342 0.9863807 -0.2927465 0.0784417 -3.732029 0.0383360 0.0274255 0.0001899 0.5033288 0.9929990
chr18 10052124 0.7279823 0.4710140 0.2569683 0.0639680 4.017140 0.0427340 0.0323713 0.0000589 0.2473169 0.9929334
chr18 8791414 0.9856789 0.7552087 0.2304702 0.0532284 4.329839 0.0418810 0.0211255 0.0000149 0.1088936 0.9928798
chr18 88230118 0.9087590 0.6296544 0.2791046 0.0731363 3.816226 0.0378690 0.0222390 0.0001355 0.4092836 0.9928358
chr18 29288185 0.9465243 0.6479676 0.2985567 0.0810847 3.682033 0.0362895 0.0250851 0.0002314 0.5672271 0.9928329
chr18 33629767 0.9834459 0.7058934 0.2775525 0.0726226 3.821848 0.0417587 0.0288577 0.0001325 0.4066557 0.9927548
chr18 3358344 0.9850959 0.6992617 0.2858341 0.0760743 3.757302 0.0417160 0.0215259 0.0001718 0.4694103 0.9927132
chr18 48906205 0.9862158 0.7208906 0.2653253 0.0676838 3.920070 0.0420633 0.0274519 0.0000885 0.3139628 0.9927093
chr18 32993959 0.5542468 0.9088841 -0.3546373 0.1043068 -3.399945 0.0626200 0.0243002 0.0006740 0.9999991 0.9926880
chr18 10052176 0.6678399 0.4112901 0.2565497 0.0641277 4.000604 0.0415192 0.0293749 0.0000632 0.2567198 0.9926811
chr18 26499750 0.9004923 0.5984799 0.3020125 0.0827545 3.649501 0.0373464 0.9894752 0.0002628 0.6165523 0.9926794
chr18 10052049 0.7564003 0.4771996 0.2792006 0.0734640 3.800507 0.0416502 0.0281231 0.0001444 0.4228374 0.9926422
chr18 10052245 0.5950548 0.3569856 0.2380691 0.0566106 4.205382 0.0415192 0.0265846 0.0000261 0.1507439 0.9926345
chr18 10052220 0.6371979 0.3869461 0.2502518 0.0616299 4.060556 0.0390249 0.0277433 0.0000490