# # # R代码从装饰图案的SigFuge来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:风格# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BiocStyle::乳胶()# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:SigFuge。Rnw: 49-56 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(SigFuge) geneAnnot <——农庄(seqnames = Rle (“chr9”, 5),范围= IRanges(开始= c(21967751, 21967751, 21970901, 21974403, 21994138),结束= c(21968241, 21968241, 21971207, 21975132, 21994490)),链= Rle(链(“-”),5))geneAnnot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:SigFuge。Rnw: 61 - 73 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(org.Hs.eg.db)库(TxDb.Hsapiens.UCSC.hg19.knownGene) genesym < - c (“CDKN2A”) geneid < -选择(org.Hs.eg。db,键= genesym keytype =“象征”,列=“ENTREZID”) txdb < - TxDb.Hsapiens.UCSC.hg19。knownGene < - exonsBy交货(txdb“基因”)geneAnnot < - ex [[geneid ENTREZID美元[1]]]geneAnnot geneAnnot <——降低(geneAnnot) geneAnnot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:SigFuge。Rnw: 78 - 99 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(Rsamtools)库(prebsdata) geneAnnot < -农庄(seqnames = Rle(“20”, 9),范围= IRanges(开始= c(49551405, 49551405, 49551405, 49558568, 49562274, 49562384, 49565166, 49571723, 49574900),结束= c(49551773, 49551773, 49551773, 49558663, 49562299, 49562460, 49565199, 49571822, 49575060)),链= Rle(链(“-”),9))bam_file1 < -执行(文件。路径(“sample_bam_files”、“input1.bam”),包=“prebsdata”) bam_file2 < -执行文件。路径(“sample_bam_files”、“input2.bam”),包=“prebsdata”) sorted1 < - sortBam (bam_file1, tempfile ()) indexBam (sorted1) sorted2 < - sortBam (bam_file2, tempfile ()) indexBam (sorted2) bam_files < - c (sorted1 sorted2) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:SigFuge。Rnw: 104 - 120 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # calcInfo < < -应用-函数(x){信息(x [[“seq”]], 2,函数(y) {y < - y [c (“A”、“c”、“G”、“T”),,放弃= FALSE)总经理汇报< - colSums (y)})信息}参数< - ApplyPileupsParam(这= geneAnnot = c (“seq”、“定性”),yieldBy =“位置”,yieldAll = TRUE) fls的< - PileupFiles (bam_files参数=参数)res < - applyPileups (fls的、calcInfo param =参数)geneDepth < - T (do.call (cbind res)) colnames (geneDepth) < - c (“Sample1”、“Sample2”) geneDepth(500:505,) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:SigFuge。Rnw: 131 - 133 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (geneAnnot)数据(geneDepth) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:SigFuge。Rnw: 139 - 144 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # genename < -“CDKN2A mdata <——geneDepth [, 101:150] SFfigure(数据= mdata locusname = genename annot = geneAnnot lplots = 1:3, savestr = genename titlestr =“CDKN2A轨迹,LUSC样本”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:SigFuge。Rnw: 179 - 183 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # genename < - - - - - -“CDKN2A”# # SFfigure (data = mdata locusname = genename, # # annot = geneAnnot lplots = 4, savestr =“CDKN2A_individual_curves”, # # titlestr =“CDKN2A轨迹,LUSC样本”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:SigFuge。Rnw: 189 - 191 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #输出<——SFpval (mdata) output@pvalnorm # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:SigFuge。Rnw: 199 - 202 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #标准< - SFnormalize (mdata)标签<——SFlabels(规范)标签[1:10]# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:SigFuge。Rnw: 207 - 219 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # exp.data < - mdata[,——(规范标志= = 1美元)]# #标签< -标签(——(规范标志= = 1美元))# # # # SFfigure (exp。数据、locusname = genename annot = geneAnnot, # #数据。labels=labels, flag=0, lplots=2, ## savestr="Raw_CDKN2A", titlestr="Raw coverage", ## pval=0) ## ## SFfigure(norm$data.norm, locusname=genename, annot=geneAnnot, ## data.labels=labels, flag=0, lplots=2, ## savestr="Norm_CDKN2A", titlestr="Normalized coverage", ## pval=0)