recurrentGenes-CopyNumberBreakPointGenes-method: Access Options recurrentGenes. This method returns a...

In GeneBreak: Gene Break Detection

Description

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

Usage

## S4 method for signature 'CopyNumberBreakPointGenes'
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 )

GeneBreak documentation built on Nov. 8, 2020, 8:18 p.m.