library(stringr)
list.dirs()
filepaths<-paste(list.dirs(),'/','abundance.tsv',sep="")[2:19]
df_tpm<-data.frame(A=1:36608)
df_counts<-data.frame(A=1:36608)
for (filepath in filepaths){
df<-read.csv(filepath,header=T,stringsAsFactors = F,sep="\t")
df5<-as.data.frame(df[,5])
colnames(df5)<-str_sub(filepath,3,12)
df_tpm<-cbind(df_tpm,df5)
df4<-as.data.frame(df[,4])
colnames(df4)<-str_sub(filepath,3,12)
df_counts<-cbind(df_counts,df4)
}
df_tpm<-df_tpm[,-1]
dim(df_tpm)
df_tpm$proteinid<-str_sub(df$target_id,21,34)
df_tpm$length<-df$length
df_tpm$eff_length<-df$eff_length
df_counts<-df_counts[,-1]
dim(df_counts)
df_counts$proteinid<-str_sub(df$target_id,21,34)
df_counts$length<-df$length
df_counts$eff_length<-df$eff_length
head(df_tpm)
head(df_counts)
write.csv(df_tpm,file="pome_peel_RNAseq_TPM.csv",quote = F,row.names = F)
write.csv(df_counts,file="pome_peel_RNAseq_est_Counts.csv",
quote=F,row.names = F)
