PlotBootstrapDistributions: PlotBootstrapDistributions

In biostuff/CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Description

Plots the generated bootstrap distribution as violin plots. Genes showing significant values are marked in a different color.

Usage

PlotBootstrapDistributions(bootList,
                           reportTables,
                           outputFolder = getwd(),
                           sampleNames = NULL,
                           save = FALSE,
                           scale = 10)

Arguments

bootList	List of bootstrapped read counts for each sample data
reportTables	List of report tables for each sample data
outputFolder	Path to the folder where the data plots will be created
sampleNames	List with sample names
save	Boolean to save the plots to the output folder
scale	Numeric scale factor

Value

A list with ggplot2 objects.

Author(s)

Thomas Wolf, Cristiano Oliveira

Examples

data(sampleReadCounts)
data(referenceReadCounts)
## Gene names should be same size as row columns
geneNames <- row.names(referenceReadCounts)

ampliconNames <- NULL

normalizedReadCounts <- CombinedNormalizedCounts(sampleReadCounts,
                                                 referenceReadCounts,
                                                 ampliconNames = ampliconNames)

# After normalization data sets need to be splitted again to perform bootstrap
samplesNormalizedReadCounts = normalizedReadCounts["samples"][[1]]
referenceNormalizedReadCounts = normalizedReadCounts["reference"][[1]]

# Should be used values above 10000
replicates <- 10

# Perform the bootstrap based analysis
bootList <- BootList(geneNames,
                     samplesNormalizedReadCounts,
                     referenceNormalizedReadCounts,
                     replicates = replicates)

backgroundNoise <- Background(geneNames,
           samplesNormalizedReadCounts,
           referenceNormalizedReadCounts,
           bootList,
           replicates = replicates)

reportTables <- ReportTables(geneNames,
             samplesNormalizedReadCounts,
             referenceNormalizedReadCounts,
             bootList,
             backgroundNoise)

PlotBootstrapDistributions(bootList, reportTables, save = FALSE)

biostuff/CNVPanelizer documentation built on May 12, 2019, 9:25 p.m.