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.

### 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 )

[Package GeneBreak version 1.16.0 Index]