plotBoxplot: Create box plot of normalized read counts

In bioinf-jku/panelcn.mops: CNV detection tool for targeted NGS panel data

Create box plot of normalized read counts

Description

Create box plot of normalized read counts

Usage

plotBoxplot(result, sampleName, countWindows, selectedGenes = NULL,
  showGene = 1, showLegend = TRUE, exonRange = NULL, ylimup = 1.15,
  thresh = 0)

Arguments

result	result object of panelcn.mops
sampleName	name of the test sample that should be displayed
countWindows	data.frame with contents of a BED file as returned by getWindows
selectedGenes	vector of names of genes of interest that should be displayed or NULL if all genes are of interest. Default = NULL
showGene	integer indicating which of the genes of interest to plot
showLegend	flag to indicate whether to display a legend with the names of the test samples. Default = TRUE
exonRange	vector of 2 positive integers to limit box plot to a certain range of exons or NULL
ylimup	numeric, maximum RC is multiplied by this value to calculate second value of ylim. Default = 1.15
thresh	numeric threshold for plotting fold change areas E.g. thresh = 0.4 plots a green rectangle above (1 + 0.4)*median for each boxplot and a red rectangle below (1 - 0.4)*median. Default of zero does not plot any colored areas.

Value

generates a boxplot of the normalized read counts

Examples

data(panelcn.mops)
sampleNames <- colnames(elementMetadata(test))
selectedGenes <- "ATM"
plotBoxplot(result = resultlist[[1]], sampleName = sampleNames[1], 
            countWindows = countWindows, selectedGenes = selectedGenes, 
            showGene = 1)

bioinf-jku/panelcn.mops documentation built on March 24, 2022, 1:19 a.m.