Man pages for plinkQC
Genotype Quality Control with 'PLINK'

check_ancestryIdentification of individuals of divergent ancestry
checkFilteringCheck and construct PLINK sample and marker filters
check_het_and_missIdentification of individuals with outlying missing genotype...
check_hweIdentification of SNPs showing a significant deviation from...
check_mafIdentification of SNPs with low minor allele frequency
checkPlinkCheck PLINK software access
check_relatednessIdentification of related individuals
checkRemoveIDsCheck and construct individual IDs to be removed
check_sexIdentification of individuals with discordant sex information
check_snp_missingnessIdentification of SNPs with high missingness rate
cleanDataCreate plink dataset with individuals and markers passing...
evaluate_check_ancestryEvaluate results from PLINK PCA on combined study and...
evaluate_check_het_and_missEvaluate results from PLINK missing genotype and...
evaluate_check_relatednessEvaluate results from PLINK IBD estimation.
evaluate_check_sexEvaluate results from PLINK sex check.
overviewPerIndividualQCOverview of per sample QC
overviewPerMarkerQCOverview of per marker QC
perIndividualQCQuality control for all individuals in plink-dataset
perMarkerQCQuality control for all markers in plink-dataset
relatednessFilterRemove related individuals while keeping maximum number of...
run_check_ancestryRun PLINK principal component analysis
run_check_heterozygosityRun PLINK heterozygosity rate calculation
run_check_missingnessRun PLINK missingness rate calculation
run_check_relatednessRun PLINK IBD estimation
run_check_sexRun PLINK sexcheck
testNumericsTest lists for different properties of numerics
plinkQC documentation built on July 15, 2021, 5:07 p.m.