Package: plinkQC 0.3.4
Hannah Meyer
plinkQC: Genotype Quality Control with 'PLINK'
Genotyping arrays enable the direct measurement of an individuals genotype at thousands of markers. 'plinkQC' facilitates genotype quality control for genetic association studies as described by Anderson and colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions accessible from 'R' and generates a per-individual and per-marker quality control report. Individuals and markers that fail the quality control can subsequently be removed to generate a new, clean dataset. Removal of individuals based on relationship status is optimised to retain as many individuals as possible in the study.
Authors:
plinkQC_0.3.4.tar.gz
plinkQC_0.3.4.zip(r-4.5)plinkQC_0.3.4.zip(r-4.4)plinkQC_0.3.4.zip(r-4.3)
plinkQC_0.3.4.tgz(r-4.4-any)plinkQC_0.3.4.tgz(r-4.3-any)
plinkQC_0.3.4.tar.gz(r-4.5-noble)plinkQC_0.3.4.tar.gz(r-4.4-noble)
plinkQC_0.3.4.tgz(r-4.4-emscripten)plinkQC_0.3.4.tgz(r-4.3-emscripten)
plinkQC.pdf |plinkQC.html✨
plinkQC/json (API)
NEWS
| # Install 'plinkQC' in R: |
| install.packages('plinkQC', repos = c('https://meyer-lab-cshl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/meyer-lab-cshl/plinkqc/issues
Last updated 3 years agofrom:a0337eb0c6. Checks:OK: 3 NOTE: 3 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | ERROR | Oct 29 2024 |
| R-4.5-linux | NOTE | Oct 29 2024 |
| R-4.4-win | NOTE | Oct 29 2024 |
| R-4.4-mac | NOTE | Oct 29 2024 |
| R-4.3-win | OK | Oct 29 2024 |
| R-4.3-mac | OK | Oct 29 2024 |
Exports:check_ancestrycheck_het_and_misscheck_hwecheck_mafcheck_relatednesscheck_sexcheck_snp_missingnesscheckFilteringcheckPlinkcleanDataevaluate_check_ancestryevaluate_check_het_and_missevaluate_check_relatednessevaluate_check_sexoverviewPerIndividualQCoverviewPerMarkerQCperIndividualQCperMarkerQCrelatednessFilterrun_check_ancestryrun_check_heterozygosityrun_check_missingnessrun_check_relatednessrun_check_sextestNumerics
Dependencies:clicolorspacecowplotcpp11data.tabledplyrfansifarvergenericsgetoptggforceggplot2ggrepelgluegridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeoptparsepillarpkgconfigplyrpolyclipR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenrlangscalessyssystemfontstibbletidyselecttweenrUpSetRutf8vctrsviridisLitewithr
Processing 1000 Genomes reference data for ancestry estimation
Rendered fromGenomes1000.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2021-02-08
Started: 2018-10-31
Ancestry estimation based on reference samples of known ethnicities
Rendered fromAncestryCheck.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2021-12-04
Started: 2018-10-23
Genotype quality control with plinkQC
Rendered fromplinkQC.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2021-02-08
Started: 2018-10-20
Processing HapMap III reference data for ancestry estimation
Rendered fromHapMap.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2021-02-08
Started: 2018-10-24
