strand_bias_test {MutationalPatterns} | R Documentation |
This function performs a Poisson test for the ratio between mutations on each strand
strand_bias_test(strand_occurrences)
strand_occurrences |
Dataframe with mutation count per strand, result from strand_occurrences() |
Dataframe with poisson test P value for the ratio between the two strands per group per base substitution type.
mut_matrix_stranded
,
strand_occurrences
,
plot_strand_bias
## 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)