QCGWAS-package: Quality Control of Genome Wide Association Study Results

In QCGWAS: Quality Control of Genome Wide Association Study Results

Quality Control of Genome Wide Association Study Results

Description

Functions for automated and manual quality control of Genome Wide Association Study results.

Details

Package:	QCGWAS
Type:	Package
Version:	1.0-9
Date:	2022-05-30
License:	GPL (>= 3)

The core of the package is the function QC_GWAS. This function carries out an automated quality-control (QC) of a Genome Wide Association Study (GWAS) results file, reporting on the data-distribution, checking the SNPs for missing and invalid data, comparing the alleles and allele-frequency to a reference, and creating QQ and Manhattan plots.

Although the number of arguments in QC_GWAS may seem overwhelming, only three of them are required to run a basic QC. The name of the file to be QC'ed should be passed to the filename argument; the directory of said file to the dir_data argument; and a header-translation table to the header_translations argument. The results will be saved in a number of files and graphs in the data directory. For a quick introduction to QCGWAS, read the quick reference guide that can be found in "R\library\QCGWAS\doc".

Author(s)

Peter J. van der Most and Ilja M. Nolte

Maintainer: Peter J. van der Most <[e-mail]>

References

Van der Most, P.J., Vaez, A., Prins, B.P., Loretto Munoz, M., Snieder, H., Alizadeh, B.Z. & Nolte, I.M. (2014). QCGWAS: A flexible R package for automated quality control of Genome-Wide Association results. Bioinformatics 30(8):1185-1186.

See Also

QC_GWAS

QCGWAS documentation built on May 30, 2022, 5:05 p.m.