healthyControlsPresenceChecker

This package allows users to verify if a specific GEO dataset contains data of healthy controls amongside data of patients.

Installation via Bioconductor

Once this package will be available on Bioconductor, it will be possibile to install it through the following commands.

Start R (version “4.1”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("healthyControlsPresenceChecker")

It will be possible to load the package with the following command:

library("healthyControlsPresenceChecker")

Usage

The usage of healthyControlsPresenceChecker is very easy. The main function healthyControlsCheck() reads two input arguments: the GEO accession code of the dataset for which the user wants to verify the presence of the healthy controls, and a verbose flag. For example, if the user wants to know if the GSE47407 dataset contains data of healthy controls, she/he can type on a terminal shell within the R environment:

outcomeGSE47407 <- healthyControlsCheck("GSE47407", TRUE)

The function will print all the intermediate messages, and eventually the outcomeGSE47407 variable will be true if healthy controls were found, or false otherwise.

Contacts

This software was developed by Davide Chicco, who can be contacted via email at davidechicco(AT)davidechicco.it