Brief instructions for the package CoExpROSMAP.

ROSMAP is a project you can access from here https://www.synapse.org/#!Synapse:syn3219045. It includes transcriptomics from more than 600 samples. Using the package https://github.com/juanbot/CoExpNets we created four co-expression networks for them.

Introduction

This package can be used through the CoExpNets package to access and analyze these networks and to create new ones.

In the package you will find networks for the following tissues

library(CoExpNets)
library(CoExpROSMAP)
CoExpROSMAP::initDb()
getAvailableNetworks()

[1] "notad" "probad" "ad" "allsamples"

Each network is compound of

• An RDS file with the network itself. When reading the object you obtain a list with moduleColors and MEs, the clustering of nodes and the module eigengenes respectively.
• A csv with the enrichment for the modules from the Gene Ontology, REACTOME and KEGG pathway annotation databases.
• The residuals (corrected by PMI, Age, Gender and Batch, with ComBat) and Surrogate variables with SVA.

Install the development version from GitHub:

Recommended that you install first CoExpNets

devtools::install_github('juanbot/CoExpNets')

And then this package, and then you install the networks so you can access them from the CoExpNets functions.

devtools::install_github('juanbot/CoExpROSMAP')
CoExpROSMAP::initDb()