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 = 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)
    )

[Package MutationalPatterns version 3.0.1 Index]