GeneBreak (version 1.2.0)

recurrentGenes,CopyNumberBreakPointGenes-method: Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold.

Description

Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold.

Usage

"recurrentGenes"(object, fdr.threshold = 0.1, summarize = TRUE, order.column = "FDR")

Arguments

object

Output of bpStats(): an object of class CopyNumberBreakPointGenes

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

Value

data.frame with genes recurrently affected by breakpoints

Examples

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 )