# Genotype Quality Control with 'PLINK'

## Documentation for package ‘plinkQC’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
checkRemoveIDs | Check and construct individual IDs to be removed
checkRF_path | Checking the path of userinputted random forest
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