## ----include=FALSE------------------------------------------------------- library(knitr) opts_chunk$set( ) ## ----include=FALSE------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----echo=FALSE, message=FALSE--------------------------------- options(width=65) set.seed(0) library(panelcn.mops) panelcn.mopsVersion <- packageDescription("panelcn.mops")$Version ## ----echo=TRUE------------------------------------------------- library(panelcn.mops) data(panelcn.mops) ## ----eval=FALSE------------------------------------------------ # bed <- "Genes_part.bed" # countWindows <- getWindows(bed) ## ----eval=FALSE------------------------------------------------ # testbam <- "SAMPLE1.bam" # test <- countBamListInGRanges(countWindows = countWindows, # bam.files = testbam, read.width = 150) ## ----eval=FALSE------------------------------------------------ # # selectedGenes <- c("ATM") # # XandCB <- test # elementMetadata(XandCB) <- cbind(elementMetadata(XandCB), # elementMetadata(control)) # # resultlist <- runPanelcnMops(XandCB, # testiv = 1:ncol(elementMetadata(test)), # countWindows = countWindows, # selectedGenes = selectedGenes) ## ----echo=FALSE,results='hide'--------------------------------- XandCB <- test elementMetadata(XandCB) <- cbind(elementMetadata(XandCB), elementMetadata(control)) selectedGenes <- "ATM" ## -------------------------------------------------------------- sampleNames <- colnames(elementMetadata(test)) resulttable <- createResultTable(resultlist = resultlist, XandCB = XandCB, countWindows = countWindows, selectedGenes = selectedGenes, sampleNames = sampleNames) (tail(resulttable[[1]])) ## ----eval=FALSE------------------------------------------------ # plotBoxplot(result = resultlist[[1]], sampleName = sampleNames[1], # countWindows = countWindows, # selectedGenes = selectedGenes, showGene = 1) ## ----fig.keep='none',echo=FALSE,results='hide'----------------- sampleNames <- colnames(elementMetadata(test)) selectedGenes <- "ATM" pdf("001.pdf", width = 10) plotBoxplot(result = resultlist[[1]], sampleName = sampleNames[1], countWindows = countWindows, selectedGenes = selectedGenes, showGene = 1) dev.off() ## -------------------------------------------------------------- bed <- system.file("extdata/Genes_part.bed", package = "panelcn.mops") countWindows <- getWindows(bed) ## ----echo=FALSE------------------------------------------------ bed <- system.file("extdata/Genes_part.bed", package = "panelcn.mops") write.table(head(read.table(bed)), row.names = FALSE, col.names = FALSE, quote = FALSE) ## ----eval=FALSE------------------------------------------------ # testbam <- "SAMPLE1.bam" # test <- countBamListInGRanges(countWindows = countWindows, # bam.files = testbam, read.width = 150) ## -------------------------------------------------------------- (test) ## ----eval=FALSE------------------------------------------------ # splitROIs(bed, "newBed.bed") ## ----eval=FALSE------------------------------------------------ # # selectedGenes <- "ATM" # # XandCB <- test # elementMetadata(XandCB) <- cbind(elementMetadata(XandCB), # elementMetadata(control)) # resultlist <- runPanelcnMops(XandCB, countWindows = countWindows, # selectedGenes = selectedGenes) ## ----eval=FALSE------------------------------------------------ # (str(resultlist[[1]])) ## ----eval=FALSE------------------------------------------------ # help(CNVDetectionResult) ## -------------------------------------------------------------- integerCopyNumber(resultlist[[1]])[1:5] ## -------------------------------------------------------------- sampleNames <- colnames(elementMetadata(test)) resulttable <- createResultTable(resultlist = resultlist, XandCB = XandCB, countWindows = countWindows, selectedGenes = selectedGenes, sampleNames = sampleNames) (tail(resulttable[[1]])) ## ----eval=FALSE------------------------------------------------ # plotBoxplot(result = resultlist[[1]], sampleName = sampleNames[1], # countWindows = countWindows, # selectedGenes = selectedGenes, showGene = 1) ## ----eval=FALSE------------------------------------------------ # toBibtex(citation("panelcn.mops"))