# #——风格,呼应= FALSE,结果= ' asis '----------------------------------- BiocStyle:减价()suppressPackageStartupMessages({库(rtracklayer)库(BiocParallel)图书馆(GenomicFiles)图书馆(TxDb.Hsapiens.UCSC.hg19.knownGene ) }) ## ---- rtracklayer-file-classes -------------------------------------------- ## rtracklayer动物园库(rtracklayer)名称(getClass(“RTLFile”)@subclasses) # #——benchmark-f0 -------------------------------------------------------- f0 < -函数(n){# #效率低下!ans < -数字()(我在seq_len (n))答< - c (ans, exp (i))答 } ## ---- 基准 ----------------------------------------------------------- f1 (n) {ans < < -功能-数字(n)(我在seq_len (n))和[[我]]< - exp (i) ans} < - f2函数(n)酸式焦磷酸钠(seq_len (n),exp) f3 < -函数(n) exp (seq_len (n )) ## ---- parallel-sleep ------------------------------------------------------ 图书馆(BiocParallel)有趣的< -函数(i) {Sys.sleep(1)我}# #系列f0 < -函数(n)拉普兰人(seq_len (n),有趣)# #平行f1 < -函数(n) bplapply (seq_len (n),有趣的)# #——csaw-packages ------------------------------------------------------- 库(GenomicAlignments)库(GenomicFiles)图书馆(BiocParallel)图书馆(Rsamtools)库(GenomeInfoDb) # #——olaps-chr ----------------------------------------------------------- 碎片弹。len < < - 50 - 110间距空空的< - # #——olaps-tileGenome“chr1” ---------------------------------------------------- fls的< - dir (~ / UseBioconductor-data / ChIPSeq / NFYA /“,”。BAM$"， full=TRUE) names(fls) <- sub(".fastq. txt ")*”、“”,basename (fls)) bfl < - BamFileList (fls的yieldSize = 1000000) # #——csaw-tiles ---------------------------------------------------------- len < - seqlengths (keepStandardChromosomes (seqinfo (bfl)))(科)瓷砖< tileGenome (len tilewidth =间距,cut.last.tile.in.chrom = TRUE) # #——收益 --------------------------------------------------------------- 收益率< -函数(x,…)readGAlignments (x) # #——地图 ----------------------------------------------------------------- map < -函数(x,瓷砖,碎片弹。len…){gr < - keepStandardChromosomes(农庄组织(x)) countOverlaps(瓷砖,调整(gr, frag.len )) } ## ---- 减少 -------------------------------------------------------------- 减少 <- `+` ## ---- reduceByYield ------------------------------------------------------- count1file < -函数(男朋友,…)reduceByYield (bf,产量、地图、减少...) ## ---- count-overlaps-parallel eval = FALSE --------------------------------- # 计数< - bplapply (count1file bfl,瓷砖=瓷砖,frag.len = frag.len) #计数< - simplify2array(计数)#暗(计数)# colSums(计数)