# #——风格,eval = TRUE,呼应= FALSE,结果= '飞机 '------------------------ 选项(max.print = 1000) stopifnot (BiocInstaller: biocVersion () = = " 2.13 ") BiocStyle::乳胶()库(knitr)美元opts_chunk组(缓存= TRUE,整洁= FALSE) # #——结果= '隐藏 '------------------------------------------------------ 库(parathyroidSE) # # - eval = FALSE ---------------------------------------------------------- ## 数据(包= " parathyroidSE ") ## ------------------------------------------------------------------------ 数据(parathyroidGenesSE) parathyroidGenesSE类(parathyroidGenesSE) (parathyroidGenesSE暗淡 ) ## ------------------------------------------------------------------------ 类(化验(parathyroidGenesSE))暗(化验(parathyroidGenesSE))测定(parathyroidGenesSE) [1:8,1:8 ] ## ------------------------------------------------------------------------ colnames (parathyroidGenesSE ) ## ------------------------------------------------------------------------ colSums(化验(parathyroidGenesSE )) ## ------------------------------------------------------------------------ sum (rowSums(化验(parathyroidGenesSE)) ! = 0 ) ## ------------------------------------------------------------------------ rowData (parathyroidGenesSE) # #------------------------------------------------------------------------ colData (parathyroidGenesSE ) ## ------------------------------------------------------------------------ 表(colData (parathyroidGenesSE)治疗美元)# #——bampaths ------------------------------------------------------------ bamdir < -系统。file("extdata"， package="parathyroidSE")文件(bamdir模式=“bam美元”,bampaths full.names = TRUE) ## ------------------------------------------------------------------------ 库(Rsamtools) gal0 < - readGAlignmentsFromBam (bampaths [1]) gal0 ## ------------------------------------------------------------------------ galp0 < - readGAlignmentPairsFromBam (bampaths [1]) galp0 ## ------------------------------------------------------------------------ 长度(galp0 ) ## ------------------------------------------------------------------------ 姓(galp0) (galp0) # #------------------------------------------------------------------------ 参数< - ScanBamParam(国旗= scanBamFlag (isDuplicate = FALSE, isNotPrimaryRead = FALSE) readGAlignmentPairsFromBam (bampaths [1], param =参数)# #——makeTranscriptDbFromBiomart eval = FALSE ----------------------------- ## ## 需要上网,大约需要6分钟。请不要尝试运行这个!# #库(GenomicFeatures) # # txdb < makeTranscriptDbFromBiomart (biomart =“运用”,# #数据集= " hsapiens_gene_ensembl ") ## ---- exonsBy eval = FALSE ------------------------------------------------- ## ex_by_gene < - exonsBy (txdb=“基因”)# GRangesList对象 ## ------------------------------------------------------------------------ 数据(exonsByGene) exonsByGene ## ------------------------------------------------------------------------ 长度(exonsByGene) # #——BamFileList --------------------------------------------------------- 库(Rsamtools) bamfile_list < BamFileList (bampaths,指数=字符 ()) ## ------------------------------------------------------------------------ read_count0 < - summarizeOverlaps (exonsByGene bamfile_list,忽视。strand=TRUE, singleEnd=FALSE) read_count0 ## ------------------------------------------------------------------------ read_count <- summarizeOverlaps(exonsByGene, bamfile_list, ignore.strand=TRUE, singleEnd=FALSE, param=param) read_count ## ------------------------------------------------------------------------ colSums(assay(read_count0)) colSums(assay(read_count))