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.
