I would like to do rna seq data for several genes, tested in control and treatment.
To do fisher.test I need a contingency table for each gene, is there a way to do this in R instead of computing a contingency table for each gene?
I am new to this so any advice can be helpful.
I have the count data and the sample Info data,
control1 treated1 control2 treat2 control3 treat3
ENSG00000000003 723 486 904 445 1170 1097
ENSG00000000005 0 0 0 0 0 0
ENSG00000000419 467 523 616 371 582 781
Where ENSG are the genes