findContextSNV: Find SNV context

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Find SNV context

Description

Given a table of SNVs, find the reference genome nucleotide bases that are at the 5' and 3' of each SNV location, according to the pyrimidine reference. For example, if the mutation is a TT[C>T]AG, then the 5' will correspond to lower genomic coordinates, with 5' context TT and the 3' will correspond to the higher genomic coordinates, with 3' context AG. Alternatively, if the mutation is a TT[A>T]AG, then the reference considered will be on the opposite strand, and the mutation and contexts will be reversed as CT[T>A]AA. It is also possible to filter the mutations in the given SNV table according to the specific pyrimidine mutation and, optionally, the first base on the 5' or 3'.

Usage

findContextSNV(
  snv_table,
  mtype = NULL,
  fiveprime = NULL,
  threeprime = NULL,
  genomev = "hg19",
  context_length = 5
)

Arguments

snv_table	data frame containing SNVs, with required columns chr, position, REF, ALT
mtype	if specified, filter mutations according to specific base changes: C>A, C>T, C>G, T>A, T>C, T>G
fiveprime	if specified, filter mutations according to specific 3': C, A, T, G. Used only if mtype is specified
genomev	genome version, hg19 or hg38
context_length	number of nucleotides on the 5' and 3' to consider

Value

table of counts of base contexts

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.