strand_bias_test {MutationalPatterns} | R Documentation

## Significance test for strand asymmetry

### Description

This function performs a Poisson test for the ratio between mutations on each strand

### Usage

    strand_bias_test(strand_occurrences)

### Arguments

`strand_occurrences` | Dataframe with mutation count per strand, result from strand_occurrences()

### Value

Dataframe with poisson test P value for the ratio between the two strands per group per base substitution type.

### See Also

`mut_matrix_stranded`, `strand_occurrences`, `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")

    ## Perform the strand bias test.
    strand_counts = strand_occurrences(mut_mat_s, by=tissue)
    strand_bias = strand_bias_test(strand_counts)

[Package MutationalPatterns version 1.99.3 Index]