### R代码来自Vignette Source'Cheungtrans.rnw'###################################################################################= as.list（hgfocuschrloc）allen = as.list（hgfocuschrlisend）pCHRS = sapply（allst，function（x）names names（x）[1]）bad = wher（sapply（pchrs，length）== 0）if（长度）（糟糕）> 0）{pCHRS = pCHRS [-bad] pCHRS = sapply（pCHRS，function（x）x）pCHRS = paste（“ chr”，pchrs，pchrs，sep =“”）allen [-bad]} st = sapply（allst，function（x）abs（x）[1]）en = sapply（allen，function（x）abs（x）[1] [1]）gra = granges（seqnames = pCHRS，，iranges（st，en））名称（gra）=名称（allst）gra = split（gra，seqnames（gra））lkg = gets（“ cheung2010”，“ chr5”）fn5 = featurenames（lkg）gra = lapply = lapply（gra = lapply（gra），函数（x）x [InterSect（names（x），fn5）]）库（snplocsdefault（），prinem.only = true）如果（！）加载（“ C1S）。if（！file.exists（“ c1s.rda”））save（c1s，file =“ c1s.rda'），如果（！exists（！exists（“ c2s”）&& file.exists.exists.exists.exists.exist（“ c2s.rda”））load（“ c2s.rda”）如果（！存在（！“ c2s”））c2s = getsnplocs（“ ch2”，as.granges = true）if（in％seqlevels中的“ ch2”％c2s））seqlevels（c2s）= gsub（“ ch”，“ chr”，seqlevels（c2s））if（！file.exists（“ c2s.rda”））save（c2s，file =“ c2s.rda”）如果（！存在（“ c3s”）&& file.exists（“ c3s.rda”））load（“ c3s.rda”）如果（！true）if（％seqlevels（C3S））seqlevels（c3s）= gsub（“ ch”，“ ch”，“ chr”，seqlevels（c3s））if（！file.exists（“ c3s.rda”）））（c3s，file =“ c3s.rda”）if（！envists（“ c4s”）&& file.exists（“ c4s.rda”））load（“ c4s.rda”）如果（！c4s = getnPlocs（“ ch4”，as.granges = true）如果（％seqlevels（c4s））seqlevels（c4s）= gsub（“ ch4s）= gsub（“ ch”，“ ch”，“ chr”，seqlevels（c4s））if（！file.exists（“ c4s.rda”））保存（c4s，file =“ c4s.rda”）如果（！ && !exists("c17s") && file.exists("c17s.rda")) load("c17s.rda") if (!exists("c17s")) c17s = getSNPlocs("ch17", as.GRanges=TRUE) if ("ch17" %in% seqlevels(c17s)) seqlevels(c17s) = gsub("ch", "chr", seqlevels(c17s)) if (!file.exists("c17s.rda")) save(c17s,file="c17s.rda") if (!exists("c19s") && !exists("c19s") && file.exists("c19s.rda")) load("c19s.rda") if (!exists("c19s")) c19s = getSNPlocs("ch19", as.GRanges=TRUE) if ("ch19" %in% seqlevels(c19s)) seqlevels(c19s) = gsub("ch", "chr", seqlevels(c19s)) if (!file.exists("c19s.rda")) save(c19s,file="c19s.rda") #if ("multicore" %in% installed.packages()[,1]) library(multicore) #system("rm -rf tsco") #tr1c = transScores("cheung2010", "chr1", ~sex, snpRanges=c1s, geneRanges=gra[["chr1"]]) #save(tr1c, file="tr1c.rda") #tr2c = transScores("cheung2010", "chr2", ~sex, snpRanges=c2s, geneRanges=gra[["chr2"]]) #save(tr2c, file="tr2c.rda") #gc() #tr3c = transScores("cheung2010", "chr3", ~sex, snpRanges=c3s, geneRanges=gra[["chr3"]]) #save(tr3c, file="tr3c.rda") #gc() #tr4c = transScores("cheung2010", "chr4", ~sex, snpRanges=c4s, geneRanges=gra[["chr4"]]) #save(tr4c, file="tr4c.rda") ################################################### ### code chunk number 2: dodo ################################################### tempfolder = function () { z = tempfile() system(paste("mkdir", z)) z } obsfold = tempfolder() permfold = tempfolder() pr17 = structure(c("209165_at", "203654_s_at", "203367_at", "201508_at", "218676_s_at", "208982_at", "202148_s_at", "214552_s_at", "214299_at", "219282_s_at"), .Names = c("AATF", "COIL", "DUSP14", "IGFBP4", "PCTP", "PECAM1", "PYCR1", "RABEP1", "TOP3A", "TRPV2")) options(verbose=TRUE) dropNAs = function (x) { if (!(is(x, "smlSet"))) stop("works only for smlSet instances") sml <- x@smlEnv$smList maf = snpStats::col.summary(sml[[1]])[, "MAF", drop = FALSE] allrs = rownames(maf) curok = which(!is.na(maf)) rm(maf) if (length(curok) == 0) stop("dropNAs eliminates all SNP on a chromosome, cannot proceed") if (length(curok) != length(allrs)) x@smlEnv$smList[[1]] = x@smlEnv$smList[[1]][, curok] rm(allrs) x } if (!exists("mgrsave")) { mgrsave = list() for (i in 1:22) { cat(i) cc17 = dropNAs(getSS("cheung2010", paste("chr", i, sep=""), probesToKeep=pr17)) mgrsave[[i]] = eqtlTests(cc17, ~sex, targdir=obsfold, runname=paste("cc17", i, sep="")) rm(cc17) gc() } save(mgrsave, file="mgrsave.rda") } set.seed(12345) if (!exists("mgrsave_perm")) { mgrsave_perm = list() for (i in 1:22) { cat(i) cc17 = dropNAs(getSS("cheung2010", paste("chr", i, sep=""), probesToKeep=pr17, wrapperEndo=permEx)) mgrsave_perm[[i]] = eqtlTests(cc17, ~sex, targdir=permfold, runname=paste("pcc17", i, sep="")) rm(cc17) gc() } save(mgrsave_perm, file="mgrsave_perm.rda") }