Reference

Main quality control functions
perIndividualQC()	Quality control for all individuals in plink-dataset
perMarkerQC()	Quality control for all markers in plink-dataset
overviewPerIndividualQC()	Overview of per sample QC
overviewPerMarkerQC()	Overview of per marker QC
cleanData()	Create plink dataset with individuals and markers passing quality control
Individual quality control functions Functions for step-by-step per-individual quality control
check_sex()	Identification of individuals with discordant sex information
check_relatedness()	Identification of related individuals
check_het_and_miss()	Identification of individuals with outlying missing genotype or heterozygosity rates
check_ancestry()	Identification of individuals of divergent ancestry
Marker quality control functions Functions for step-by-step per-marker quality control
check_snp_missingness()	Identification of SNPs with high missingness rate
check_maf()	Identification of SNPs with low minor allele frequency
check_hwe()	Identification of SNPs showing a significant deviation from Hardy-Weinberg- equilibrium (HWE)
Quality control helper functions Helper functions for step-by-step per-individual quality control: accesible to the user, but recommended use via per-individual check_* functions.
run_check_sex()	Run PLINK sexcheck
evaluate_check_sex()	Evaluate results from PLINK sex check.
run_check_heterozygosity()	Run PLINK heterozygosity rate calculation
run_check_missingness()	Run PLINK missingness rate calculation
evaluate_check_het_and_miss()	Evaluate results from PLINK missing genotype and heterozygosity rate check.
run_check_relatedness()	Run PLINK IBD estimation
evaluate_check_relatedness()	Evaluate results from PLINK IBD estimation.
run_check_ancestry()	Run PLINK principal component analysis
evaluate_check_ancestry()	Evaluate results from PLINK PCA on combined study and reference data
General helper functions
checkPlink()	Check PLINK software access
testNumerics()	Test lists for different properties of numerics
relatednessFilter()	Remove related individuals while keeping maximum number of individuals