GWASinspector
Tools for (automated and manual) quality control of the results of Genome Wide Association Studies
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. It will also generate cleaned, harmonized GWAS files ready for meta-analysis.
GWASinspector has many features. Detailed instructions on how to use the package can be found in the manual. A sample vignette is also available from here.
Installation
The latest stable version is available from CRAN repository.
License
GWASinspector is licensed under the GNU General Public License, version 3.
Requirements
R 3.2 or higher
Contributors
The following people contributed to the design and development of GWASinspector:
Citation
Please cite the following paper if you use GWASinspector in your research:
Ani et al. GWASinspector: comprehensive quality control of genome-wide association study results. Bioinformatics (2021). doi:
10.1093/bioinformatics/btaa1084Disclaimer: We hope that GWASinspector will be of significant help in future researches, however, it is published WITHOUT ANY WARRANTY.
News
May 2023
Package function names were renamed by replacing "." with "_". For example, setup.inspector() is renamed to setup_inspector(). Please refere to package manual for the full list of function names.
Nov. 2022
XLSX package was replaced with OPENXLSX package. This was done because the former package is Java dependent and didn't work properly on some systems.
Apr. 2021
The reference database from 1000G project (GRCh38) is temporarily removed due to prbolems in the original data. More information available from here.
Feb. 2021
- Variant matching process has improved.
- Harmonized id (hID) column can be added to the data files. This is required for matching of the variants with no RS number.
Oct. 2020
New reference database available from 1000G project (GRCh38). Allele frequency of the variants in five population groups and rsIDs are included.
Examples
The latest stable version of the package can be installed from CRAN repository using the
install.packages function in
R, e.g.
install.packages("GWASinspector")
Check if the package is correctly installed and required modules are available on the system
library(GWASinspector)
system_check()
Load the modified configuration file and run the analysis.
job <- setup_inspector("/home/user/config.ini")
job
job <- run_inspector(job)
result_inspector(job)
A demo function is available to explain the package and explore its features.
demo_inspector('/sample_dir')
Download
SQLite database files should be unzipped before using in the software.
* allele_ref_std_population parameter in the configuration file must be filled using one of the available options.
Frequently asked questions
Q:
Can I use this package on Mac OS?
Yes, GWASinspector is a cross platform package and is tested on Windows, Linux and Mac operating systems.
Q:
I can't find any HTML report files in the output folder?
First, check the log file for any warnings or errors. Then check if html_report parameter is set as TRUE in the configuraton file. Also, make sure that Pandoc module is installed and available from R by using the system_check() command. Pandoc is a free and open-source document converter which will be installed alongside with RStudio. More information can be found at: https://pandoc.org
Q:
Pandoc is installed and available from R, but I get this error in the log file: "Connection can not be made."
This error is due to an access permission problem on your system. Run R or RStudio as administrator.
SNPannotator package
A package for investigating the functional characteristics of selected SNPs and genomic region in their vicinity.
This package is now available from CRAN. Please refer to the Manual for more information.
Supplementary material