strand_occurrences: Count occurrences per base substitution type and...

Description Usage Arguments Value See Also Examples

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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