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: 1.0-8
Date: 2014-02-11
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 <p.j.van.der.most@umcg.nl>

References

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

See Also

QC_GWAS