README.md

In Sage-Bionetworks/CMSclassifier: prediction of the Consensus Molecular Subtype (CMS) of colorectal carcinomas based on log2_scaled Gene Expression Profiles (GEP)

CMSclassifier

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]]

Sage-Bionetworks/CMSclassifier documentation built on May 9, 2019, 12:10 p.m.