plot_strand_bias: Plot strand bias per base substitution type per group

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Plot strand bias per base substitution type per group

Description

Plot strand bias per base substitution type per group

Usage

plot_strand_bias(strand_bias, colors = NA, sig_type = c("fdr", "p"))

Arguments

strand_bias	data.frame, result from strand_bias function
colors	Optional color vector with 6 values for plotting
sig_type	The type of significance to be used. Possible values: * 'fdr' False discovery rate. A type of multiple testing correction.; * 'p' for regular p values.

Value

Barplot

See Also

mut_matrix_stranded, strand_occurrences, strand_bias_test plot_strand

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"
))


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)

## Plot the strand bias.
plot_strand_bias(strand_bias)

## Use multiple (max 3) significance cutoffs.
## This will vary the number of significance stars.
strand_bias_multistars <- strand_bias_test(strand_counts,
  p_cutoffs = c(0.05, 0.01, 0.005),
  fdr_cutoffs = c(0.1, 0.05, 0.01)
)
plot_strand_bias(strand_bias_multistars)

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.