sequenza (version 1.0.5)

VarScan2abfreq: Import varscan output files, to be able to use it with sequenza algorithm.

Description

Create an abfreq file from VarScan2 output files.

Usage

VarScan2abfreq(varscan.somatic, varscan.copynumber = NULL)

Arguments

varscan.somatic

data.frame from the output file of varscan somatic.

varscan.copynumber

data.frame from the output file of varscan copynumber. it is not required. default NULL

Details

It is possible to run sequenza with the output of VarScan2, as version 2.3.6, but also previous release might be working as well. The function will create a data.frame with the abfreq format, as explained in read.abfreq page.