checkFiltering          Check and construct PLINK sample and marker
                        filters
checkPlink              Check PLINK software access
checkRemoveIDs          Check and construct individual IDs to be
                        removed
check_ancestry          Identification of individuals of divergent
                        ancestry
check_het_and_miss      Identification of individuals with outlying
                        missing genotype or heterozygosity rates
check_hwe               Identification of SNPs showing a significant
                        deviation from Hardy-Weinberg- equilibrium
                        (HWE)
check_maf               Identification of SNPs with low minor allele
                        frequency
check_relatedness       Identification of related individuals
check_sex               Identification of individuals with discordant
                        sex information
check_snp_missingness   Identification of SNPs with high missingness
                        rate
cleanData               Create plink dataset with individuals and
                        markers passing quality control
evaluate_check_ancestry
                        Evaluate results from PLINK PCA on combined
                        study and reference data
evaluate_check_het_and_miss
                        Evaluate results from PLINK missing genotype
                        and heterozygosity rate check.
evaluate_check_relatedness
                        Evaluate results from PLINK IBD estimation.
evaluate_check_sex      Evaluate results from PLINK sex check.
overviewPerIndividualQC
                        Overview of per sample QC
overviewPerMarkerQC     Overview of per marker QC
perIndividualQC         Quality control for all individuals in
                        plink-dataset
perMarkerQC             Quality control for all markers in
                        plink-dataset
relatednessFilter       Remove related individuals while keeping
                        maximum number of individuals
run_check_ancestry      Run PLINK principal component analysis
run_check_heterozygosity
                        Run PLINK heterozygosity rate calculation
run_check_missingness   Run PLINK missingness rate calculation
run_check_relatedness   Run PLINK IBD estimation
run_check_sex           Run PLINK sexcheck
testNumerics            Test lists for different properties of numerics
