filter_counts: Filter alleles based on raw counts

In mrc-ide/MIPanalyzer: Filtering and analysis of MIP data

Filter alleles based on raw counts

Description

Drop any allele for which the number of read counts is below a given threshold. Coverage is adjusted to account for dropped reads.

Usage

filter_counts(
  x,
  count_min = 2,
  description = "filter individual allele counts"
)

Arguments

x	object of class mipanalyzer_biallelic or mipanalyzer_multiallelic.
count_min	alleles with fewer than this many counts are dropped.
description	brief description of the filter, to be saved in the filter history.

mrc-ide/MIPanalyzer documentation built on Jan. 17, 2024, 7:16 p.m.