cmapR (CMap R code)
Parsing and utility functions for analyzing CMap data. For documentation, please visit this project's ReadTheDocs page. There is also a tutorial available here. To learn more about the CMap project at the Broad Institute, please visit clue.io.
Install instructions
Dependencies are listed in DESCRIPTION
Docker
A docker container with cmapR can be obtained here: https://hub.docker.com/r/cmap/cmapr. This may be preferable for those who would like to use the package without installing on their system.
Installing from source
Perhaps the simplest way is to install directly from github using devtools::install_github("cmap/cmapR"). Note that this requires having previously installed the devtools package.
The script install_cmapR.R takes care of installing all the dependencies and then running devtools::install_github("cmap/cmapR"), so you can simply source this script after cloning this repository.
Alternatively, you can point your R's install.packages function at a tarball of the cmapR archive. You can generate this archive by cloning this repository and doing the following:
# make a gzip tar ball of the repo
R CMD build cmapR
# makes cmapR_1.0.tar.gz
# check that the package is ok
R CMD check cmapR_1.0.tar.gz
Once you have created the tarball, open an R terminal and execute the following:
install.packages("cmapR_1.0.tar.gz", type="source", repos=NULL)
library("cmapR")
You can also source individual files as needed instead of installing the entire package.
# For example, just load the IO methods
source("cmapR/R/io.R")
Citation information
If you use GCTx and/or cmapR in your work, please cite Enache et al.