2021-04-27

最新推荐文章于 2024-04-28 16:07:29 发布

sayhello1025

最新推荐文章于 2024-04-28 16:07:29 发布

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分类专栏：生信技巧

本文链接：https://blog.csdn.net/sayhello1025/article/details/116209216

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在这l
ibrary('limma')
symbol <- data.table::fread('./bulk data/02.tcga/gencode.v22.annotation.gene.probeMap',data.table = F)
rownames(symbol) <- symbol[,1]
tcga_fpkm <- data.table::fread('./bulk data/02.tcga/TCGA-BRCA.htseq_fpkm.tsv/TCGA-BRCA.htseq_fpkm.tsv',data.table = F)
rownames(tcga_fpkm) <- tcga_fpkm[,1]
same <- intersect(row.names(symbol),row.names(tcga_fpkm))
tcga_B <- cbind(symbol[same,],tcga_fpkm[same,])
tcga_B <- tcga_B[,-1]
rt<- tcga_B[,-c(2:6)]
rt=as.matrix(rt)
rownames(rt)=rt[,1]
exp=rt[,2:ncol(rt)]
dimnames=list(rownames(exp),colnames(exp))
data=matrix(as.numeric(as.matrix(exp)),nrow=nrow(exp),dimnames=dimnames)
data=avereps(data)
data=data[rowMeans(data)>0,]
data[1:4][1:4]里插入代码片