Significance test for transcriptional strand asymmetry

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Description

This function performs a Poisson test for the ratio between mutations on the transcribed and untranscribed strand

Usage

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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 transcribed and untrascribed strand per group per base substitution type.

See Also

mut_matrix_stranded, strand_occurrences, 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")

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

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