# #——风格,回声= FALSE,结果= '飞机 '------------------------------- knitr: opts_chunk设置(eval = as.logical (Sys美元。采用“KNITR_EVAL”,“真正的”)),缓存= as.logical (Sys。采用“KNITR_CACHE”,“真正的”)))选项(宽度= 75 ) ## ---- 消息= FALSE ---------------------------------------------------- 库(Biostrings ) ## ------------------------------------------------------------------------ 头(方法(class = " DNAStringSet "))(通用= " reverseComplement方法 ") ## ----消息= FALSE ------------------------------------------------------ 库(GenomicRanges ) ## ------------------------------------------------------------------------ gr < -农庄(“A”,IRanges (c(10年,20年,22),宽度= 5),“+”)转变(gr, 1) # intra-range范围(gr) # inter-range减少(gr) # inter-range snp < -农庄(“A”,IRanges (c(24) 11日,17日,宽度= 1)findOverlaps (snps, gr) # between-range setdiff(范围(gr), gr) #内含子的# #,SummarizedExperiment消息= FALSE ------------------------------- 库(SummarizedExperiment)库(气道 ) ## ------------------------------------------------------------------------ 数据(气管)气道colData(气管)头(化验(气管))气道,<- as(seqinfo(rowRanges(气道))，“农庄”)(“14”)气道(气道% % chr14 ,] ## ------------------------------------------------------------------------ colSums(化验(气道 )) ## ---- 消息= FALSE ------------------------------------------------------ 库(ggplot2 ) ## ------------------------------------------------------------------------ ridx < - rowSums(化验(气管))> 0se < -气道(ridx] ave_log_expr < - rowMeans(日志(1 +试验(se)))(资源< -宠物猫::装在框内(ave_log_expr,“基因”,“ave_log_expr”)ggplot(资源描述,aes (ave_log_expr)) + geom_density () ## ------------------------------------------------------------------------ il = IntegerList(样本(26岁,5),样本(26日7) il > 7任何(il > 7) il (il > 7)重新刊登(字母(unlist (il)], ) ## ------------------------------------------------------------------------ DataFrame (i = 1:2, = IntegerList(样本(5)、(7)),dna = DNAStringSet (c(“ATCG”、“AAACGGG”)),gr =农庄组织(c(“chr1:1-20”,“chr20:10-30 ")) ) ## ---- 消息= FALSE ---------------------------------------------------- 库(rtracklayer ) ## ------------------------------------------------------------------------ 数据(cpgIslands,包= " Gviz”)cpgIslands名称< -字母[1:10]cpgIslands美元得分< -样本(10)cpgIslands bed_file < - tempfile (fileext =“轮回”):(bed_file)出口(cpgIslands bed_file)猫(readline (bed_file), 9 =“\ n”)进口(bed_file ) ## ------------------------------------------------------------------------ gtf < -系统。file(package = "气道"，"extdata"， " homo_sapiens . grch37 .75 _子集。gtf" ) import(gtf) ## see also `GenonmicFeatures::makeTxDbFromGFF()` ## ------------------------------------------------------------------------ library(GenomicAlignments) ## ------------------------------------------------------------------------ fls <- dir( system.file(package = "airway", "extdata"), pattern = "bam", full.names = TRUE ) readGAlignments(fls[1]) ## ---- message = FALSE---------------------------------------------------- library(GenomicAlignments) ## ------------------------------------------------------------------------ fl <- dir( system.file(package = "airway", "extdata"), pattern = "bam", full.name = TRUE ) fl[1] readGAlignments(fl[1]) ## hack: index the bam file in-place invisible(indexBam(fl[1])) which <- GRanges(c("1:11053773-11072770", "1:11362290-11386194")) param <- ScanBamParam(which = which, what = "seq") readGAlignments(fl[1], param = param) ## ------------------------------------------------------------------------ bf <- BamFile(fl[1], yieldSize = 5000) open(bf) repeat { galn <- readGAlignments(bf) if (length(galn) == 0) break ## do work message(length(galn)) } close(bf) ## ------------------------------------------------------------------------ sessionInfo()