# #——回声= FALSE,结果=“隐藏”,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - suppressPackageStartupMessages({库(ChIPpeakAnno)库(EnsDb.Hsapiens.v75)图书馆(TxDb.Hsapiens.UCSC.hg19.knownGene)图书馆(org.Hs.eg.db)}) knitr:: opts_chunk设置美元(警告= FALSE,消息= FALSE) # #——快速入门- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #首先,加载ChIPpeakAnno包库(ChIPpeakAnno) # #进口- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - < -道路系统。文件(“extdata”、“Tead4。broadPeak”,包= " ChIPpeakAnno”)的峰值< - toGRanges(路径,格式=“broadPeak”)峰[1:2]# #——annotationData - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -图书馆(EnsDb.Hsapiens.v75) annoData < toGRanges (EnsDb.Hsapiens.v75) annoData[1:2] # #——注释- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #保持在同一风格seqlevelsStyle seqnames(山峰)< - seqlevelsStyle (annoData) # #做注释,最近的TSS庵野< - annotatePeakInBatch(山峰,annotationData = annoData)伊斯兰教纪元[1:2]#饼图可以用来演示重叠峰的特点。pie1(表(伊斯兰教纪元insideFeature美元))# #——addIDs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(org.Hs.eg.db)伊斯兰教纪元< - addGeneIDs(伊斯兰教纪元,orgAnn = " org.Hs.eg。db”, feature_id_type = " ensembl_gene_id ", IDs2Add = c(“象征”)负责人(伊斯兰教纪元)# # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -图书馆(TxDb.Hsapiens.UCSC.hg19.knownGene) annoData < toGRanges (TxDb.Hsapiens.UCSC.hg19.knownGene) annoData [1:2] seqlevelsStyle(山峰)< - seqlevelsStyle (annoData) # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -伊斯兰教纪元< - annotatePeakInBatch(山峰,AnnotationData = annoData输出=“重叠”,FeatureLocForDistance =“TSS bindingRegion = c(-2000、300))伊斯兰教纪元美元符号<——xget(伊斯兰教纪元特性,美元org.Hs.egSYMBOL)头(伊斯兰教纪元)# #——fig.height = 3, fig.width = 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -伊斯兰教纪元< - annotatePeakInBatch(山峰,AnnotationData = annoData输出=“nearestBiDirectionalPromoters bindingRegion = c(-5000、500))伊斯兰教纪元美元符号< - xget(伊斯兰教纪元特性,美元org.Hs.egSYMBOL)伊斯兰教纪元(庵野峰美元= =“peak12725”) # #——trackViewer - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(trackViewer) gr < - <高峰的峰值(“peak12725”)开始(gr) < -开始(gr) - 5000端(gr) < -端(gr) + 5000 (.Platform $ OS。类型! =“窗口”)= {peak12725 < - importScore(文件系统。文件(“extdata”、“Tead4。大佬”,包= " ChIPpeakAnno”),范围=高峰,格式=“大佬”)其他}{# # rtracklayer不能导入大佬文件在Windows加载(file.path(目录名(路径),“cvglist.rds”)) peak12725 < -视图(cvglists [[“Tead4”]] [[as.character (seqnames(峰值)))),(峰值)开始,结束(峰值))peak12725 < - viewApply (peak12725 as.numeric) tmp < -代表(峰值、宽度(峰值))宽度(tmp) < - 1 tmp < -转变(tmp转变= 0:(宽度(峰值)1)mcols (tmp) < - peak12725 colnames (mcols (tmp)) < -“分数”peak12725 < -新(“跟踪”,dat = tmp name = " peak12725 "类型=“数据”,格式=“床”)}trs < - geneModelFromTxdb (TxDb.Hsapiens.UCSC.hg19。knownGene org.Hs.eg。db, gr)名称(trs) < -粘贴(酸式焦磷酸钠(trs、功能(.ele) .ele@name)、名称(trs), 9 =”:“) optSty < - optimizeStyle(专辑曲目(peak12725、trs heightDist = c (。3、7)),主题=“bw”) viewTracks (optSty跟踪美元,gr = gr, viewerStyle = optSty $风格)