enrichment_depletion_test: Test for enrichment or depletion of mutations in genomic...
In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description Usage Arguments Value See Also Examples

View source: R/enrichment_depletion_test.R

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

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

`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

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

genomic_distribution, plot_enrichment_depletion

## 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)
)