estimate 计算肿瘤纯度
2019-01-21 本文已影响21人
一路向前_莫问前程_前程似锦
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
