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GWASinspector (version 1.7.1)

Comprehensive and Easy to Use Quality Control of GWAS Results

Description

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.

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Version

Install

install.packages('GWASinspector')

Monthly Downloads

793

Version

1.7.1

License

GPL-3

Maintainer

Alireza Ani

Last Published

May 6th, 2024

Functions in GWASinspector (1.7.1)

get_config

Copies the template configuration file to the local machine
get_headerTranslation

Copies the template header translation table to the local machine
compare_GWASs

Compare summary statistics of GWAS result files
StudyList-class

An S4 class to represent a list of inspected GWAS study result files.
demo_inspector

Runs an example QC
GWASinspector

Comprehensive and Easy to Use Quality Control of GWAS Results
manhattan_plot

Creates the Manhattan plot
Study-class

An S4 class to represent an inspected GWAS study result file.
Inspector-class

An S4 class to represent the methods and parameters for inspecting a list of GWAS study result files.
result_inspector

Displays a brief report after running the QC pipeline
system_check

Checks which required and optional packages are available
run_inspector

Runs the QC pipeline on a set of GWAS result files
setup_inspector

Importing a configuration file into R for setting the pipeline parameters