R: Count occurrences per base substitution type and strand

strand_occurrences {MutationalPatterns}

R Documentation

Count occurrences per base substitution type and strand

Description

For each base substitution type and strand the total number of mutations and the relative contribution within a group is returned.

Usage

strand_occurrences(mut_mat_s, by)

Arguments

`mut_mat_s`	192 feature mutation count matrix, result from 'mut_matrix_stranded()'
`by`	Character vector with grouping info, optional

Value

A data.frame with the total number of mutations and relative contribution within group per base substitution type and strand

Examples

## See the 'mut_matrix_stranded()' example for how we obtained the
## following mutation matrix.
mut_mat_s <- readRDS(system.file("states/mut_mat_s_data.rds",
                                    package="MutationalPatterns"))

## Load a reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

tissue <- c("colon", "colon", "colon",
            "intestine", "intestine", "intestine",
            "liver", "liver", "liver")

strand_counts = strand_occurrences(mut_mat_s, by=tissue)