recurrentGenes,CopyNumberBreakPointGenes-method {GeneBreak} | R Documentation |
Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold.
## S4 method for signature 'CopyNumberBreakPointGenes' recurrentGenes(object, fdr.threshold = 0.1, summarize = TRUE, order.column = "FDR")
object |
Output of bpStats(): an object of class |
fdr.threshold |
A numeric Genes with lower FDR are returned |
summarize |
A logical to determine whether to only output a selection of columns |
order.column |
Name of the column to sort output on |
data.frame with genes recurrently affected by breakpoints
data( copynumber.data.chr20 ) data( ens.gene.ann.hg18 ) bp <- getBreakpoints( copynumber.data.chr20 ) bp <- bpFilter( bp ) bp <- addGeneAnnotation( bp, ens.gene.ann.hg18 ) bp <- bpGenes( bp ) bp <- bpStats( bp ) recurrentGenes( bp )