Meta-Analysis of Gene Expression Data

A pipeline for the meta-analysis of gene expression data. We have assembled several analysis and plot functions to perform integrated multi-cohort analysis of gene expression data (meta- analysis). Methodology described in: < http://biorxiv.org/content/early/2016/08/25/071514>.

This is README space for metaIntegrator_public. To be filled with a README if necessary, or for internal use if required.

What is this repository for?

• This repository is for building and testing the metaIntegrator_public R package

Who do I talk to?

• Either create an issue, email adityamr [at] stanford.edu, or email hayneswa [at] stanford.edu

How do I install the MetaIntegrator package?

For the current version on CRAN:

install.packages("MetaIntegrator")

For the current development version:

Run the following lines in R:

library(devtools)

install_bitbucket("khatrilab/metaIntegrator_public", auth_user=USERNAME, password=PASSWORD)

where USERNAME and PASSWORD are your bitbucket username and password.

If you get "ERROR: dependency ‘deapathways’ is not available for package ‘MetaIntegrator’", follow these steps:

download the deapathways_1.0.tar.gz file (which is stored in metaIntegrator_public/inst).

install deapathways, either by going to the command line, navigating to the folder containing
the tar.gz file in the command line and running R CMD INSTALL deapathways_1.0.tar.gz,
or by running install.packages(PATH_TO_FILE, repos = NULL, type="source")
where PATH_TO_FILE is the path to the deapathways_1.0.tar.gz file

Documentation

To read the Vignette go to: http://khatrilab.bitbucket.org/MetaIntegratorVignette/