### R代码来自Vignette Source'Vignettes/copdsexualdimorphism/inst/doc/lgrc_sdcd_methp.rnw'#################################################################################（x，y）粘贴（x，y，sep =“”）p.cutoff = 0.01 data（lgrc.methp）data（lgrc.meta）data（lgrc.sdcd.genes）sampleid = names = names（methp）[grepl（grepl）“^lt”，名称（methp），perl = true）= methp $ name colnames（仅限）= sampleid ####################################################################################bed = GRanges(seqnames=Rle("chr" %+% sdcd.genes$chromosome_name), ranges=IRanges(start=sdcd.genes$start_position, end=sdcd.genes$end_position, names=sdcd.genes$ensembl_gene_id），strand = rle（strand（sdcd.genes $ strand））））methp = subset（methp，！chr in％c（“ chrx”，“ chry”）））methp.bed = granges = granges（seqnames = rle（methp $ chr），ranges = iranges（start = methp $ start，end = methp $ end，names = methp $ name））窗口= 2e4 sum（countoverlaps（sdcd.genes.bed.bed，resize size size size size（methp.bed，window，window），fix =“ center”））！= 0）＃397 sdcd基因具有w/in 10kb sum（countoverLaps（sdcd.genes.bed），resize（methp.bed，2e6）！= 0）sum（countoverLaps（resize（resize）（resize（resize））methp.bed，窗口，fix =“ center”），sdcd.genes.bed）！= 0）＃892 vmr具有10kb sdcd.genes.genes.genes.vmr.bed的sdcd基因，fix =“ center”），sdcd.genes.bed）＃892 vmrs具有sdcd genes sdcd.genes.genes.vmr = names（sdcd.genes.vmr.bed）################################################-98 ############################# design = cbind(ctrl=1, gender=as.integer(meta[sampleID,"GENDER"] == "1-Male"), age=meta[sampleID,"age"], pkyr=meta[sampleID,"pkyrs"]) good.idx = apply(design,1,function(x){!any(is.na(x))}) & meta[sampleID,"diagmaj"] == "2-COPD/Emphysema" copd.fit = lmFit(logit(only.methp)[sdcd.genes.vmr,good.idx], design[good.idx,]) copd.fit = eBayes(copd.fit) good.idx = apply(design,1,function(x){!any(is.na(x))}) & meta[sampleID,"diagmaj"] == "3-Control" ctrl.fit = lmFit(logit(only.methp)[sdcd.genes.vmr,good.idx], design[good.idx,]) ctrl.fit = eBayes(ctrl.fit) ################################################### ### code chunk number 4: lgrc_sdcd_methp.Rnw:103-106 ################################################### copd.ctrl.gender.beta.diff.genes = sdcd.vmr(copd.fit, ctrl.fit, "gender", sdcd.genes, annotate=TRUE, annotate.with="genes", fdr.cutoff=0.05, file.prefix="copd.ctrl.gender", class.names=c("copd","ctrl")) copd.ctrl.gender.beta.diff.vmr = copd.ctrl.gender.beta.diff.genes$vmr ################################################### ### code chunk number 5: lgrc_sdcd_methp.Rnw:113-134 (eval = FALSE) ################################################### ## vmr.sdcd.gene = sapply(as.character(copd.ctrl.gender.beta.diff.genes$genesymbol), function(g) { ## this.vmr.genes = unlist(strsplit(g,",")) ## this.vmr.sdcd = this.vmr.genes[which(this.vmr.genes %in% sdcd.genes$hgnc_symbol)] ## if (length(this.vmr.sdcd) > 1) { ## print(g %+% " has more than one SDCD") ## better.sdcd = as.character(sdcd.genes[sdcd.genes$hgnc_symbol %in% this.vmr.sdcd,"hgnc_symbol"][which.min(sdcd.genes[sdcd.genes$hgnc_symbol %in% this.vmr.sdcd,"copd.ctrl.p.adj"])]) ## print("Keeping " %+% better.sdcd %+% " because of copd.ctrl.p.adj") ## this.vmr.sdcd = better.sdcd ## } ## if (length(this.vmr.sdcd) == 0) this.vmr.sdcd = NA ## return(this.vmr.sdcd) ## } ) ## interesting.vmrs = copd.ctrl.gender.beta.diff.genes$vmr[vmr.sdcd.gene %in% sdcd.genes$hgnc_symbol] ## interesting.vmrs.genes = vmr.sdcd.gene[vmr.sdcd.gene %in% sdcd.genes$hgnc_symbol] ## names(interesting.vmrs.genes) = interesting.vmrs ## copd.bool = meta[sampleID,"diagmaj"] == "2-COPD/Emphysema" ## male.bool = meta[sampleID,"GENDER"] == "1-Male" ## for (ivmr in interesting.vmrs) { ## this.gene = interesting.vmrs.genes[ivmr] ## do.sdcd.boxplot(ivmr, only.methp, copd.bool, male.bool, symbol=this.gene, filename=this.gene %+% "." %+% ivmr %+% ".pdf") ## } ################################################### ### code chunk number 6: lgrc_sdcd_methp.Rnw:139-140 ################################################### sessionInfo()