checkRemoveIDs: Check and construct individual IDs to be removed

In plinkQC: Genotype Quality Control with 'PLINK'

Description

checkRemoveIDs checks that the file names with the individuals to be filtered can be found. It reads the corresponding files, combines the selected individuals into one data.frame and compares these to all individuals in the analysis.

Usage

checkRemoveIDs(prefix, remove_individuals = NULL, keep_individuals)

Arguments

prefix	[character] Prefix of PLINK files, i.e. path/2/name.bed, path/2/name.bim and path/2/name.fam.
remove_individuals	[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.
keep_individuals	[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

Value

data.frame containing family (FID) and individual (IID) IDs of individuals to be removed from analysis.

plinkQC documentation built on July 15, 2021, 5:07 p.m.