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. |