# #——包括= FALSE ------------------------------------------------------------ 库(knitr) opts_chunk美元 ( ) ## ---- 包括= FALSE ------------------------------------------------------------ 库(knitr) opts_chunk美元设置(和谐= TRUE ) ## ---- 回声= FALSE,消息= FALSE --------------------------------- 选项(宽度= 65)set.seed图书馆(panelcn.mops) panelcn(0)。mopsVersion < - packageDescription (panelcn.mops) $ # #版本——回声= TRUE ------------------------------------------------- 库(panelcn.mops)数据(panelcn.mops) # # - eval = FALSE ------------------------------------------------ # <——“Genes_part睡。床上“# countWindows < - getWindows(床)# # - eval = FALSE ------------------------------------------------ # testbam <——“SAMPLE1。# test <- countBamListInGRanges(countWindows = countWindows， # bam. bat " # test <- countBamListInGRanges(countWindows = countWindows， # bam. bat ")Files = testbam，已读取。宽度= 150)# # - eval = FALSE ------------------------------------------------ # # selectedGenes < - c (ATM) # # XandCB < -测试# elementMetadata (XandCB) < - cbind (elementMetadata (XandCB), # elementMetadata(控制))# # resultlist < runPanelcnMops (XandCB # testiv = 1: ncol (elementMetadata(测试),# countWindows = countWindows,# selectedGenes = selectedGenes) # #——回声= FALSE,结果= '隐藏 '--------------------------------- XandCB < -测试elementMetadata (XandCB) < - cbind (elementMetadata (XandCB) elementMetadata(控制))selectedGenes <——“自动取款机 " ## -------------------------------------------------------------- sampleNames < - colnames (elementMetadata(测试))resulttable < createResultTable (resultlist = resultlist XandCB = XandCB countWindows = countWindows selectedGenes = selectedGenes,sampleNames = sampleNames)(尾(resulttable [[1 ]])) ## ---- eval = FALSE ------------------------------------------------ # plotBoxplot(结果= resultlist [[1]], sampleName = sampleNames [1], # countWindows = countWindows # selectedGenes = selectedGenes showGene = 1) # #——无花果。保持=‘没有’,回声= FALSE,结果= '隐藏 '----------------- sampleNames < - colnames (elementMetadata(测试))selectedGenes < -“取款机”pdf(“001. pdf”,宽度= 10)plotBoxplot(结果= resultlist [[1]], sampleName = sampleNames [1], countWindows = countWindows selectedGenes = selectedGenes showGene = 1) dev.off () ## -------------------------------------------------------------- 床上< -执行(“extdata / Genes_part。床”,包= " panelcn.mops”)countWindows < - getWindows(床)# #——回声= FALSE ------------------------------------------------ 床上< -执行(“extdata / Genes_part。床”,包= " panelcn.mops”)write.table(头(read.table(床)),row.names = FALSE, col.names = FALSE,引用= FALSE) # # - eval = FALSE ------------------------------------------------ # testbam <——“SAMPLE1。# test <- countBamListInGRanges(countWindows = countWindows， # bam. bat " # test <- countBamListInGRanges(countWindows = countWindows， # bam. bat ")Files = testbam，已读取。宽度= 150 ) ## -------------------------------------------------------------- ( 测试)# # - eval = FALSE ------------------------------------------------ # newBed.bed splitROIs(床上。 ") ## ---- eval = FALSE ------------------------------------------------ # # selectedGenes < -“取款机”# # XandCB < -测试# elementMetadata (XandCB) < - cbind (elementMetadata (XandCB), # elementMetadata(控制))# resultlist < - runPanelcnMops (XandCB countWindows = countWindows,# selectedGenes = selectedGenes) # # - eval = FALSE ------------------------------------------------ # ( str (resultlist [[1 ]])) ## ---- eval = FALSE ------------------------------------------------ # 帮助(CNVDetectionResult ) ## -------------------------------------------------------------- integerCopyNumber (resultlist [[1]]) [1:5 ] ## -------------------------------------------------------------- sampleNames < - colnames (elementMetadata(测试))resulttable < createResultTable (resultlist = resultlist,XandCB = XandCB countWindows = countWindows selectedGenes = selectedGenes sampleNames = sampleNames)(尾(resulttable [[1 ]])) ## ---- eval = FALSE ------------------------------------------------ # plotBoxplot(结果= resultlist [[1]], sampleName = sampleNames [1], # countWindows = countWindows # selectedGenes = selectedGenes showGene = 1) # # - eval = FALSE ------------------------------------------------ # toBibtex(引用(“panelcn.mops”))