strand_occurrences: Count occurrences per base substitution type and strand

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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 = NA)

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

See Also

mut_matrix_stranded, plot_strand, plot_strand_bias

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)

MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.