run.inspector

This is the main function of the package for running the QC algorithm on a set of GWAS result files.
It requires an object of class Inspector which should be created by <code>setup.inspector</code>.
Check the package vignette and tutorial for more details on this topic.

When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.

Alireza Ani

GWASinspector

Comprehensive and Easy to Use Quality Control of GWAS Results

Peter J. van der Most

Ahmad Vaez

Ilja M. Nolte

run.inspector function

<dl><dt>inspector</dt>
<dd>An instance of Inspector class. Check <code>setup.inspector</code> for more details.</dd>
<dt>verbose</dt>
<dd>logical. If FALSE, no messages will show up in the terminal and are only saved in the log file.</dd>
<dt>test.run</dt>
<dd>logical. If TRUE, only the first 1000 lines of each data file are loaded and analyzed;
plots and saving the cleaned output dataset are skipped. Default value is FALSE.</dd></dl>

Arguments

Runs the QC pipeline on a set of GWAS result files — run.inspector

<dl>

<dt>inspector</dt>
<dd>An instance of Inspector class. Check <code>setup.inspector</code> for more details.</dd>


<dt>verbose</dt>
<dd>logical. If FALSE, no messages will show up in the terminal and are only saved in the log file.</dd>


<dt>test.run</dt>
<dd>logical. If TRUE, only the first 1000 lines of each data file are loaded and analyzed;
plots and saving the cleaned output dataset are skipped. Default value is FALSE.</dd>

</dl>

run.inspector: Runs the QC pipeline on a set of GWAS result files

Description

Usage

Value

Arguments