createResultTable: Creates a user readable result table for the test samples of...
In bioinf-jku/panelcn.mops: CNV detection tool for targeted NGS panel data

createResultTable

R Documentation

Creates a user readable result table for the test samples of the genes of interest

Description

Creates a user readable result table for the test samples of the genes of interest

Usage

createResultTable(resultlist, XandCB, countWindows, selectedGenes = NULL,
  sampleNames)

Arguments

`resultlist`	result object of runPanelcnMops
`XandCB`	GRanges object of combined read counts of test samples and control samples as returned by getRCRanges or countBamListInGRanges
`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
`sampleNames`	names of the test samples (basename of the BAM files)

Value

a data.frame containing the results for the test samples within the genes of interest

Examples

data(panelcn.mops)
XandCB <- test
elementMetadata(XandCB) <- cbind(elementMetadata(XandCB), 
                                elementMetadata(control))
sampleNames <- colnames(elementMetadata(test))
selectedGenes <- "ATM"
resulttable <- createResultTable(resultlist = resultlist, XandCB = XandCB, 
                                    countWindows = countWindows, 
                                    selectedGenes = selectedGenes, 
                                    sampleNames = sampleNames)

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