cmapR: modified by Loyal

Tools and utilities for loading and analyzing methylation data. The GCT object and .gctx file format are a way to keep data and associated row and column metadata together at all times, including operations for reading, writing and subsetting these data.

For a tutorial of the available functions in this package, see tutorial/loyal_basics.R

Install instructions

Create a conda environment for the package by installing R and the dependencies. Here I use mamba for increased speed in creating the environment. You can also do this in an environment that already exists or has R installed.

mamba create -n cmapr -c conda-forge -c r -c bioconda r-base=4.1.2
conda activate cmapr

Clone the github repo to a convenient location, and install the package locally by running the install R script.

git clone https://github.com/Cellular-Longevity/cmapR.git
cd cmapR
Rscript install_cmapR.R

In order to use the functions pulling data from AWS, you need to have the AWS_ACCESS_KEY_ID, AWS_DEFAULT_REGION and AWS_SECRET_ACCESS_KEY environment variables configured. You can set these by running aws configure or modifying the ~/.aws/credentials file.

You should then be all set up! Please file an issue with any problems installing or using this package.

Citation information

This repo was originally developed as cmap/cmapR. "Parsing and utility functions for analyzing CMap data. To learn more about the CMap project at the Broad Institute, please visit clue.io." If you use GCTx and/or cmapR in your work, please cite Enache et al.