# # - eval = FALSE --------------------------------------------------------------- # # 对齐:#样品。Fastq ->样本。sam # #CONVERT: # samtools view -b -S sample。Sam -o样品。bam # #SORT: # samtools SORT sample。bam sample_sorted # #INDEXING: # samtools index sample_sorted。bam # # - eval = TRUE ---------------------------------------------------------------- 库(wavClusteR)文件名< -系统。文件("extdata"， "example. ")bam”,包= " wavClusteR”)bam < - readSortedBam(文件名=文件名)bam # # - eval = TRUE ---------------------------------------------------------------- countTable < - getAllSub (Bam minCov = 10)头(countTable ) ## ---- 无花果。宽度= 5,fig.height = 5, fig.align =‘中心’,eval = TRUE ----------------- = " TC plotSubstitutions (countTable亮点 " ) ## ---- eval = FALSE --------------------------------------------------------------- # 模型< - fitMixtureModel (countTable替换= " TC ") ## ---- eval = TRUE ---------------------------------------------------------------- 数据(模型)str(模型)# #——无花果。宽度= 7,fig.height = 4.5, fig.align =‘中心’,eval = TRUE --------------- ( 支持< - getExpInterval(模型、贝叶斯= TRUE ) ) ## ---- 无花果。width=7, fig.height=4.5, fig.align='center'， eval=TRUE--------------- (support <- getExpInterval(model, bayes = FALSE, leftProb = 0.9, rightProb = 0.9)) ## ----宽度= 7,fig.height = 5, fig.align =‘中心’,eval = TRUE ----------------- plotSubstitutions (countTable,突出=“TC”模型 ) ## ---- eval = TRUE ---------------------------------------------------------------- highConfSub < - getHighConfSub (countTable =支持,替换=“TC”)负责人(highConfSub ) ## ---- eval = FALSE --------------------------------------------------------------- # highConfSub < - getHighConfSub (countTable # supportStart = 0.2, # supportEnd = 0.7,#替换=“TC) #头(highConfSub ) ## ---- eval = TRUE ---------------------------------------------------------------- 覆盖< -覆盖(Bam)覆盖chrX # #美元——eval = TRUE ---------------------------------------------------------------- 集群< getClusters (highConfSub = highConfSub覆盖率=覆盖率,sortedBam = Bam,阈值= 1, cores = 1 ) clusters ## ----eval=TRUE---------------------------------------------------------------- clusters <- getClusters( highConfSub = highConfSub, coverage = coverage, sortedBam = Bam, cores = 1 ) clusters ## ----eval=TRUE---------------------------------------------------------------- require(BSgenome.Hsapiens.UCSC.hg19) wavclusters <- filterClusters( clusters = clusters, highConfSub = highConfSub, coverage = coverage, model = model, genome = Hsapiens, refBase = "T", minWidth = 12) wavclusters ## ----eval=FALSE--------------------------------------------------------------- # exportHighConfSub( highConfSub = highConfSub, # filename = "hcTC.bed", # trackname = "hcTC", # description = "hcTC" ) ## ----eval=FALSE--------------------------------------------------------------- # exportClusters( clusters = wavclusters, # filename = "wavClusters.bed", # trackname = "wavClusters", # description = "wavClusters" ) ## ----eval=FALSE--------------------------------------------------------------- # exportCoverage( coverage = coverage, filename = "coverage.bigWig" ) ## ----eval=FALSE--------------------------------------------------------------- # txDB <- makeTxDbFromUCSC(genome = "hg19", tablename = "ensGene") ## ----eval=FALSE--------------------------------------------------------------- # annotateClusters( clusters = wavclusters, # txDB = txDB, # plot = TRUE, # verbose = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # getMetaGene( clusters = wavclusters, # txDB = txDB, # upstream = 1e3, # downstream = 1e3, # nBins = 40, # nBinsUD = 10, # minLength = 1, # plot = TRUE, # verbose = TRUE ) ## ----eval=FALSE--------------------------------------------------------------- # getMetaTSS( sortedBam = Bam, # txDB = txDB, # upstream = 1e3, # downstream = 1e3, # nBins = 40, # unique = FALSE, # plot = TRUE, # verbose = TRUE ) ## ----fig.width=5, fig.height=5, fig.align='center', eval=TRUE----------------- plotSizeDistribution( clusters = wavclusters, showCov = TRUE, col = "skyblue2" ) ## ----fig.width=5, fig.height=5, fig.align='center', eval=FALSE---------------- # plotStatistics( clusters = wavclusters, # corMethod = "spearman", # lower = panel.smooth ) ## ----eval=TRUE---------------------------------------------------------------- sessionInfo()