CheckSeqContextInVCF: Check that the sequence context information is consistent...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Check that the sequence context information is consistent with the value of the column REF.

Description

Check that the sequence context information is consistent with the value of the column REF.

Usage

CheckSeqContextInVCF(vcf, column.to.use)

Arguments

vcf	In-memory VCF as a data.frame; must be an SBS or DBS VCF.
column.to.use	The column name as a string of the column in the VCF with the context information.

Value

Throws error with location information if the value of REF is inconsistent with the value of seq.21bases. Assumes the first base of the reference allele is at position (size(<context string>)-1)/2, and generates error if this is not an integer. Indices are 1-based.

ICAMS documentation built on June 22, 2024, 6:47 p.m.