metapredict

metapredict enables meta-analysis of gene expression using the elastic net (i.e., glmnet). For technical details, please check out the paper.

If you just want to process microarray data and don’t need to merge the expression data to perform a meta-analysis, then check out seeker, which makes fetching, processing, and normalizing transcriptome data even simpler.

Installation

1. Install BiocManager.

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

2. If you use RStudio, go to Tools → Global Options… → Packages → Add… (under Secondary repositories), then enter:

   • Name: hugheylab
   • Url: https://hugheylab.github.io/drat/

   You only have to do this once. Then you can install or update the package by entering:

   BiocManager::install('metapredict')

   Alternatively, you can install or update the package by entering:

   BiocManager::install('metapredict', site_repository = 'https://hugheylab.github.io/drat/')

Usage

Go through the vignettes to

• prepare the data for the example meta-analysis,
• run the example meta-analysis, and
• see how to run your own meta-analysis.

For help on using specific functions, consult the reference documentation.