AddSeqContext: Add sequence context to a data frame with mutation records

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

Add sequence context to a data frame with mutation records

Description

Add sequence context to a data frame with mutation records

Usage

AddSeqContext(df, ref.genome, seq.context.width = 10, name.of.VCF = NULL)

Arguments

df	An input data frame storing mutation records of a VCF file.
ref.genome	A ref.genome argument as described in ICAMS.
seq.context.width	The number of preceding and following bases to be extracted around the mutated position from ref.genome. The default value is 10.

Value

A copy of the input data.frame with a new column added that contains sequence context information.

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