CMS classifier for mouse models.
The complete code used to generate figures and perform analyses in the article: "Enterocyte-like differentiation defines the metabolic gene signatures of CMS3 colorectal cancers and provides a therapeutic vulnerability." , along with the processed data required to run the scripts, can be accessed on GitHub.com/atorang/mouseCMS_Scripts, and synapse.org (id = syn53040345); respectively. GitHub.com/atorang/mouseCMS_Scripts
An example data set is provided to explain how to work with mouseCMS R package and mouseCMSclassifier function.
To install the mouseCMS package use the following code:
devtools::install_github("atorang/mouseCMS")
The example data exprs.test is a data.frame object with log2-transformed expression levels. Rows are genes and columns are samples. Ensembl IDs are used.
library("mouseCMS")
res<-mouseCMSclassifier(exprs.test, perform.log2=FALSE)