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