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