GeneBreak: A package for gene breakpoint detection on copy number abberation data

Description

The GeneBreak package performs cohort based recurrent gene breakpoint detection on copynumber data. It is possible to use the output of the function CGHcall from the package CGHcall or the function callBins from the package QDNAseq as the input for this analysis.

GeneBreak functions

Analysis starts with the function getBreakpoints and continues with:
bpFilter to exclude certain breakpoints from the analysis
addGeneAnnotation to add gene location information
bpGenes to determine which features (probes/bins) are related to which genes
bpStats to determine which gene breaks are recurrent in the cohort