Genotype Quality Control with 'PLINK'

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Documentation for package ‘plinkQC’ version 0.3.4

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

Help Pages

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