estimate 计算肿瘤纯度

library(utils)
rforge <- "http://r-forge.r-project.org"
install.packages("estimate", repos=rforge, dependencies=TRUE)
library(estimate)

OvarianCancerExpr <- system.file("extdata", "sample_input.txt",
                                 package="estimate")
read.table(OvarianCancerExpr)[1:4,1:4]

filterCommonGenes(input.f=OvarianCancerExpr, 
                  output.f="OV_10412genes.gct", 
                  id="GeneSymbol")

estimateScore(input.ds = "OV_10412genes.gct",
              output.ds="OV_estimate_score.gct", 
              platform="affymetrix")

plotPurity(scores="OV_estimate_score.gct", samples="s516", 
           platform="affymetrix")

scores=read.table("OV_estimate_score.gct",skip = 2,header = T)
rownames(scores)=scores[,1]
scores=t(scores[,3:ncol(scores)])
scores