flag_alleles: Flag Alleles

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

Description

Flag alleles that are present in too many samples at high variant allele frequencies as potential errors.

Usage

flag_alleles(
  variants,
  metadata = FALSE,
  starting_percentile = 99,
  interval = 0.001
)

Arguments

variants	VRanges object from get_flagged_alleles
metadata	Logical. Determine whether or not to keep the metadata (annotations) when returning flagged alleles
starting_percentile	Lower VAF percentile to start looking for alleles to flag. Default is 99, but can use 95 if you want to flag more alleles (more conservative)
interval	VAF interval to iterate through for flagging alleles. Default is 0.001

Value

This function returns a VRanges object with the following information:

• seqnames

• ranges

• ref

• alt

• refdepth

• altdepth

• sampleNames

• metadata (optional)

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