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plinkQC
View on CRAN: Click
here
Download and install plinkQC package within the R console
Install from CRAN:
install.packages("plinkQC")
Install from Github:
library("remotes")
install_github("cran/plinkQC")
Install by package version:
library("remotes")
install_version("plinkQC", "0.3.4")
Attach the package and use:
library("plinkQC")
Maintained by
Hannah Meyer
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-11-04
Latest Update: 2021-07-15
Description:
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) . 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.
How to cite:
Hannah Meyer (2018). plinkQC: Genotype Quality Control with 'PLINK'. R package version 0.3.4, https://cran.r-project.org/web/packages/plinkQC
Previous versions and publish date:
Other packages that cited plinkQC R package
View plinkQC citation profile
Other R packages that plinkQC depends,
imports, suggests or enhances
Functions, R codes and Examples using
the plinkQC R package
Some associated functions: checkFiltering . checkPlink . checkRemoveIDs . check_ancestry . check_het_and_miss . check_hwe . check_maf . check_relatedness . check_sex . check_snp_missingness . cleanData . evaluate_check_ancestry . evaluate_check_het_and_miss . evaluate_check_relatedness . evaluate_check_sex . overviewPerIndividualQC . overviewPerMarkerQC . perIndividualQC . perMarkerQC . plinkQC . relatednessFilter . run_check_ancestry . run_check_heterozygosity . run_check_missingness . run_check_relatedness . run_check_sex . testNumerics .
Some associated R codes: applyQC.R . individualQC.R . markerQC.R . plinkQC.R . utils.R . Full plinkQC package functions and examples
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