I am very new to DESEQ2 and I am struggling to create the initial Deseq2 dataset. I have a zip file with HT-seq counts for 5 days and each has a certain number of repeats, there are 22 files in total in the zip file. Each with the counts from each studied day. I don't understand how to get this into a format to where I can do differential analysis across all days to find out which day a certain gene I am looking at has the highest significant expression or differentially expressed.
This is what I've found online so far:
sampleFiles <- grep("D",list.files(directory),value=TRUE)
so this identifies which files I want
sampleCondition <- sub("(.*D06,*D13).*","\\1",sampleFiles)
then I want the conditions to be the days but I can't get this code to do that?
sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition) sampleTable$condition <- factor(sampleTable$condition)
I would really appreciate any help I'm very lost with this