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Tumor purity.R
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Tumor purity.R
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## Reference DOI: 10.1038/ncomms9971
library(dplyr)
library(estimate)
library(data.table)
library(org.Hs.eg.db)
source("function/estimate_.R")
setwd("/media/CADD/longfei/project/sex_web/")
tpm_dat <- fread("rawdata/toil/TcgaTargetGtex_rsem_gene_tpm.gz",data.table=FALSE)
#phenotype_dat <- fread("rawdata/toil/TcgaTargetGTEX_phenotype.txt.gz")
ensg <- tpm_dat$sample %>% substr(.,1,15)
gene_symbol <- AnnotationDbi::mapIds(x <- org.Hs.eg.db,
keys = ensg,
column = "SYMBOL",
keytype = "ENSEMBL",
multiVals="first"
)
tpm_matrix <- tpm_dat[!is.na(gene_symbol) & !duplicated(gene_symbol),-1]
gene_symbol <- na.omit(gene_symbol) %>% unique()
rownames(tpm_matrix) <- gene_symbol
filter_mat <- filterCommonGenes_(tpm_matrix)
estimateRes<- estimateScore_(filter_mat,
platform="affymetrix")
estimateRes <- t(estimateRes)
saveRDS(estimateRes,file = "result/purity.rds")