I used exacttest
(edgeR) on some RNA seq data. I need to make a table that depicts the 10 genes with the smallest q- values, their log fold change, and their raw expression values. I have the q-values stored in a numeric vector, the fold change can be found by using exacttest$table$logFC, and I have the raw expression values .
I am not sure how to put all of these together in a table and sort them. I tried sorting the q-values using sort(qvalues)
, this certainly displays the top 10 smallest qvalues but in the vector they are not associated with a gene ID so I don't think I can do this. Any ideas on how to do this?
Thanks
Thank you for the reply, I solved my problem in the meantime. I had to do it this certain way as part of an assignment. I don't see $FDR as an option, perhaps I need to load another package to have that feature?