QCEWAS-package: Quality Control of Epigenome-Wide Association Study Results

In QCEWAS: Fast and Easy Quality Control of EWAS Results Files

Quality Control of Epigenome-Wide Association Study Results

Description

Functions for automated and manual quality control of Epigenome-Wide Association Study results.

Details

Package:	QCEWAS
Type:	Package
Version:	1.2-3
Date:	2023-02-03
License:	GPL (>= 3)

When combining the results of multiple Epigenome-Wide Association Studies (EWAS) into a meta-analysis, it is recommended to run a quality check (QC) over the individual files first. This is not only to check if the individual results are valid, reliable, and of high quality, but also to ensure that they are comparable between cohorts. The QCEWAS package was developed to automate this process.

The core function of QCEWAS is EWAS_QC. This function accepts the filename of a single EWAS results file and performs a thorough quality check. For more information, see the EWAS_QC help page. The function EWAS_series is a wrapper function that accepts multiple file names, and then runs EWAS_QC for all of them. It also generates a few additional plots to compare the results of the files, allowing the user to spot differences in effect-size distribution or standard errors.

The functions EWAS_plots and P_correlation are subroutines of EWAS_QC that can also be called by the user to perform specific QC tasks.

QCEWAS also includes a Quick-Start Guide. A link to the guide is provided when the package is loaded into R.

Author(s)

P.J. van der Most, Leanne K. Kupers and Ilja M. Nolte

Maintainer: P.J. van der Most <[e-mail]>

QCEWAS documentation built on Feb. 16, 2023, 10:30 p.m.