ancestry_prediction     Predicting sample superpopulation ancestry
checkFiltering          Check and construct PLINK sample and marker
                        filters
checkLoadingMat         Checking the path of the loading matrix
checkPlink              Check PLINK software access
checkPlink2             Check PLINK2 software access
checkRF_path            Checking the path of userinputted random forest
checkRemoveIDs          Check and construct individual IDs to be
                        removed
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
convert_from_vcf        Converting VCF data files into PLINK v1.9 and
                        PLINK v2.0 data files
convert_to_plink2       Converting PLINK v1.9 data files into PLINK
                        v2.0 data files
evaluate_ancestry_prediction
                        Predicting sample superpopulation ancestry
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
pruning_ld              Pruning of SNPs in Linkage Disequilibrium
relatednessFilter       Remove related individuals while keeping
                        maximum number of individuals
rename_variant_identifiers
                        Renaming variants
run_ancestry_format     Running functions to format data for ancestry
                        prediction
run_ancestry_prediction
                        Projecting the study data set onto the PC space
                        of the reference dataset
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
