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GWASinspector (version 1.6.1)

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

1.6.1

License

GPL-3

Maintainer

Alireza Ani

Last Published

January 9th, 2023

Functions in GWASinspector (1.6.1)

Study-class

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

Comprehensive and Easy to Use Quality Control of GWAS Results
get.config

Copies the template configuration file to the local machine
get.headerTranslation

Copies the template header translation table to the local machine
Inspector-class

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

Runs an example QC
result.inspector

Displays a brief report after running the QC pipeline
manhattan.plot

Creates the Manhattan plot
compare.GWASs

Compare summary statistics of GWAS result files
StudyList-class

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