correct_pvalues: p-value correction

In andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Description

Apply multiple testing correction (FDR or Bonferroni) to model p-values for each position. If input is VRangesList, then pvalue correction will be done on a sample-by-sample basis. If input is VRanges, then pvalue correction will be done across all samples. For mutation calling in a narrow genomic range of specified hotspots, we recommend correcting across all samples. For mutation calling across all genomic positions sequenced, we recommend applying correction by sample.

Usage

correct_pvalues(variant_calls, method = "bonferroni")

Arguments

variant_calls	VRangesList or VRanges object from call_all_variants output
method	pvalue correction method to pass onto p.adjust

Value

This function returns a VRangesList or VRanges object with a new metadata column: corrected_pvalue

Examples

## Not run: 
variants_corrected <- correct_pvalue(variant_calls = variants, method = 'bonferroni')

## End(Not run)

andygxzeng/ECSI documentation built on Feb. 6, 2021, 8:53 a.m.