Genotype Quality Control with 'PLINK'
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Documentation for package ‘plinkQC’ version 1.0.1
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 |
| 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_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 |