Genotype Quality Control with 'PLINK'


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Documentation for package ‘plinkQC’ version 0.3.2

Help Pages

checkPlink Check PLINK software access
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