mutations_to_catalog: Given chromosome, position, reference, and altered allele...

In eyzhao/SignIT: What the Package Does (One Line, Title Case)

Description

Given chromosome, position, reference, and altered allele values, returns a mutation catalog. Assumes SNV mutation types conforming to the standard 96-element mutation types.

Usage

mutations_to_catalog(chr, pos, ref, alt, genome = NULL)

Arguments

chr	Character vector of chromosomes (must match genome seqlevels)
pos	Integer vector of mutation positions
ref	Character vector of reference alleles (A, C, G, or T)
alt	Character vector of mutated alleles (A, C, G, or T)
genome	BSgenome object from which to derive trinucleotide context sequences

Value

Data frame with columns mutation_type and count

eyzhao/SignIT documentation built on Dec. 6, 2019, 11:45 a.m.