get_RPOB: Calculate read pair orientation bias

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

get_RPOB calculates, for each C:G > T:A variant present in vcf_filename, two read pair orientation bias (RPOB) metrics: FdeamC and strand orientation bias (SOB). The calculation is based on data retrieved from vcf_filename.

Usage

get_RPOB(vcf_filename, samplename, ...)

Arguments

vcf_filename	character string naming the path to the input vcf, i.e. the vcf file containing the variants to classify. This file must have been generated with Mutect2, either in tumor only or tumor/normal mode with strand bias annotation enabled.
samplename	character string naming the sample in vcf_filename. This must match the name given to the sample when running Mutect2. It can be obtained by calling get_samplename on vcf_filename.
...	additional arguments not to be checked.

Value

List containing two numeric vectors: FDeamC and SOB. Each element in the vectors corresponds to a C:G > T:A variant in vcf_filename and the elements are ordered by appearance in vcf_filename.

mmaitenat/ideafix documentation built on Sept. 18, 2021, 7:55 a.m.