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

enrichment_depletion_test {MutationalPatterns}

R Documentation

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 = c())

Arguments

`x`	data.frame result from genomic_distribution()
`by`	Optional grouping variable, e.g. tissue type

Value

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

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.
distr_test2 <- enrichment_depletion_test(distr)