CNV detection tool for targeted NGS panel data

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Documentation for package ‘panelcn.mops’ version 1.31.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.