icgc

library(readr)
library(limma)
library(tidyverse)
 setwd('H:\\迅雷下载\\icgc-dataset-1618818706447\\sam')
 rt<-read_tsv('exp_seq.tsv')
 rt1<-select(rt,c('icgc_donor_id','gene_id','normalized_read_count'))
 rt1%>%
   group_by(icgc_donor_id) %>% 
   mutate(id=1:n()) %>%
   spread(icgc_donor_id,normalized_read_count)->rt2
 
 rt2$id<-NULL

 rm(rt,rt1) 
 
 
 rt=as.matrix(rt2)
 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)>0.4,]
 rm(rt,rt2,exp,dimnames) 
 
data<-as.data.frame(data) 
data$id<-rownames(data)
data1<-filter(data,id==c('FGF14-AS2','LINC01082','LINC02041'))
mer<-intersect(data$id,c('FGF14-AS2','LINC01082','LINC02041'))