README.md

LUMP

LUMP score for tumor purity estimation according to Dvir Aran, Marina Sirota,and Atul J. Buttea. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015; 6:8971

Install

devtools::install_github("yeswzc/LUMP")

Usage example

1. download the source code
2. load the R function
3. use it :

library(minfi)
library(minfiData)
library(LUMP)

baseDir <- system.file("extdata", package="minfiData")
targets <- read.metharray.sheet(baseDir)
RGset <- read.metharray.exp(targets = targets)
#Mset <- preprocessRaw(RGset) 
Mset = preprocessQuantile(RGset)
beta = getBeta(Mset)

lump(beta)