Functions for automated and manual quality control of Genome Wide Association Study results.
|License:||GPL (>= 3)|
The core of the package is the function
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
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".
Peter J. van der Most and Ilja M. Nolte
Maintainer: Peter J. van der Most <email@example.com>
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.