enrichment_depletion_test: Test for enrichment or depletion of mutations in genomic...

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

Test for enrichment or depletion of mutations in genomic regions

Description

This function aggregates mutations per group (optional) and performs an enrichment depletion test.

Usage

enrichment_depletion_test(x, by = NA, p_cutoffs = 0.05, fdr_cutoffs = 0.1)

Arguments

x	data.frame result from genomic_distribution()
by	Optional grouping variable, e.g. tissue type
p_cutoffs	Significance cutoff for the p value. Default: 0.05
fdr_cutoffs	Significance cutoff for the fdr. Default: 0.1

Value

data.frame with the observed and expected number of mutations per genomic region per group (by) or sample

See Also

genomic_distribution, plot_enrichment_depletion

Examples

## See the 'genomic_distribution()' example for how we obtained the
## following data:
distr <- readRDS(system.file("states/distr_data.rds",
  package = "MutationalPatterns"
))

tissue <- c(rep("colon", 3), rep("intestine", 3), rep("liver", 3))

## Perform the enrichment/depletion test by tissue type.
distr_test <- enrichment_depletion_test(distr, by = tissue)

## Or without specifying the 'by' parameter, to pool all samples.
distr_single_sample <- enrichment_depletion_test(distr)

## Use different significance cutoffs for the pvalue and fdr
distr_strict <- enrichment_depletion_test(distr,
  by = tissue,
  p_cutoffs = 0.01, fdr_cutoffs = 0.05
)

## Use multiple (max 3) significance cutoffs.
## This will vary the number of significance stars.
distr_multistars <- enrichment_depletion_test(distr,
  by = tissue,
  p_cutoffs = c(0.05, 0.01, 0.005),
  fdr_cutoffs = c(0.1, 0.05, 0.01)
)

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