« 於: 四月 05, 2017, 05:39:55 am »
basedir <- "E:/GeneExpression/SRP073050-Monocytes-counts"
setwd(basedir)
sample = c("S080","S081","S082","S083","S084","S085")
for (i in 1:length(sample) ) {
filename <- paste(sample[i], '.counts', sep = "", collapse = "")
exp_table <-read.table(filename, header = F, stringsAsFactors = FALSE)
if (i==1){#read only once
df<-read.table(filename, header = F, stringsAsFactors = FALSE)
names(df) <- c("Gene", sample[i])
}
else{
df2<-read.table(filename, header = F, stringsAsFactors = FALSE)
df[sample[i]] <-df2[2]
}
}
write.csv(df, file = "SRP073050.csv")
library(DESeq2)
files = c("S080.counts","S081.counts","S082.counts","S083.counts","S084.counts","S085.counts")
cond = c("A","A","A","B","A","A")
sTable = data.frame(sampleName = files, fileName = files, condition = cond)
dds <-DESeqDataSetFromHTSeqCount(sampleTable=sTable, directory = "E:/GeneExpression/SRP073050-Monocytes-counts", design = ~condition)
dds <- DESeq(dds)
res <- results(dds)
summary(res)
write.csv(as.data.frame(res),file="SRP073050-FCGR3B.csv")
plotMA(res, main="DESeq2", ylim=c(-2,2))
