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 = 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)

[Package MutationalPatterns version 3.0.1 Index]