CNV detection tool for targeted NGS panel data


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Documentation for package ‘panelcn.mops’ version 1.26.0

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control GRanges object of countWindows with read counts for control samples as elementMetadata.
countBamListInGRanges Get read counts for a list of BAM files and given count windows
countWindows result object of getWindows - a data.frame with the contents of the provided BED file with an additional gene name and exon name column
createResultTable Creates a user readable result table for the test samples of the genes of interest
getWindows Convert BED file into data.frame of count windows
panelcn.mops Core copy number detection algorithm for targeted NGS panel data
plotBoxplot Create box plot of normalized read counts
read.width read width used for calculating RCs of test and control
resultlist result object of runPanelcnMops - a list of instances of "CNVDetectionResult"
runPanelcnMops Full copy number detection for targeted NGS panel data for multiple samples
splitROIs Split (larger) ROIs into multiple smaller (overlapping) bins and create new BED file
test GRanges object of countWindows with read counts for a test sample as elementMetadata.