Count occurrences per base substitution type and transcriptional strand

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Description

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

Usage

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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 transcriptional strand (T = transcribed strand, U = untranscribed strand).

See Also

mut_matrix_stranded, plot_strand, plot_strand_bias

Examples

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## 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)

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