assign_allele: Assign alleles bases on allele frequency and depth

In surh/HMVAR: Human Microbiome Variant Analysis in R

Description

Internal

Usage

assign_allele(
  dat,
  depth_thres = 1,
  freq_thres = 0.5,
  sequence = FALSE,
  na_rm = TRUE
)

Arguments

dat	A data.frame or tibble
depth_thres	depth_threshold
freq_thres	freq_threshold
sequence	Should the actual nucleodites be returned? If FALSE the allele column will contain 'major' or 'minor'. If TRUE, the allele column will contain the actual nucleotide
na_rm	Should sites from samples that could not be assigned be returned?

Value

Same tibble as dat but with an allele column

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.