mc.sumContext: Compute frequencies and proportions of mutations with context

In EmilieT/mutcraft: functions to decipher and plot mutation data

Description

Compute frequencies and proportions of mutations with context

Usage

mc.sumContext(mutnet.obj, base.ref.col = "ref.allele",
  base.alt.col = "alt.allele", base.3p.col = "base.3p",
  base.5p.col = "base.5p", trinuc.pc, symetrize = c(TRUE, FALSE)[1])

Arguments

mutnet.obj	A dataframe of mutation info
base.ref.col	Name of the column with the reference allele in dataframe
base.alt.col	Name of the column with the alternative allele in dataframe
base.3p.col	Name of the column with the base after the mutation in dataframe
base.5p.col	Name of the column with the base before the mutation in dataframe
trinuc.pc	Array of the proportion of each trinucleotide in the genome (for normalisation)
symetrize	Boolean to symetrize reversable mutations or not

Value

A dataframe with each mutation and context, with frequencies and proportions

EmilieT/mutcraft documentation built on May 6, 2019, 3:47 p.m.