An R package and an example data set are provided to run the CMSclassifier.
To install the CMSclassifier, install from github using devtools:
library(devtools)
install_github("Sage-Bionetworks/CMSclassifier")
To run the demo below, you will need a Synapse account and the Synapse R client installed:
source('http://depot.sagebase.org/CRAN.R')
pkgInstall("synapseClient")
Both classifiers (Random forest and single sample) expect data formatted according to the example data set provided:
library(synapseClient)
library(CMSclassifier)
synapseLogin()
sampleData <- read.table(synGet("syn4983432")@filePath, sep="\t",header = TRUE,row.names = 1,check.names=FALSE)
Rfcms <- CMSclassifier::classifyCMS(t(sampleData),method="RF")[[3]]
SScms <- CMSclassifier::classifyCMS(t(sampleData),method="SSP")[[3]]