Man pages for HannahVMeyer/plinkQC
Genotype Quality Control with 'PLINK'
| check_ancestry | Identification of individuals of divergent ancestry |
| checkFiltering | Check and construct PLINK sample and marker filters |
| check_het_and_miss | Identification of individuals with outlying missing genotype... |
| check_hwe | Identification of SNPs showing a significant deviation from... |
| check_maf | Identification of SNPs with low minor allele frequency |
| checkPlink | Check PLINK software access |
| check_relatedness | Identification of related individuals |
| checkRemoveIDs | Check and construct individual IDs to be removed |
| 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... |
| evaluate_check_ancestry | Evaluate results from PLINK PCA on combined study and... |
| evaluate_check_het_and_miss | Evaluate results from PLINK missing genotype and... |
| 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 |
| plinkQC | plinkQC |
| relatednessFilter | Remove related individuals while keeping maximum number of... |
| 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 |
