Hi, I have the following read count table

> rawCountTable <- read.table(paste0(basedir,"Htseq_read_counts/Sporobolus_pyramadalis_read_counts_mod_gene_names_modified.tsv"), header=TRUE,
+                             row.names=1)
> head(rawCountTable)
          X1916.MJO.0001_1 X1916.MJO.0002_1 X1916.MJO.0003_1 X1916.MJO.0004_1
sp0055008                9                5               10                2
sp0052637               32               16               27               18
sp0025247               50               73               67               63
sp0025250                9                5                5               17
sp0025268              141              117              107              104
sp0025270                0                0                0                0

and in this paper they added annotation with help

> y <- DGEList(fc$counts, group=group)
> y$genes <- fc$annotation[, "Length", drop=FALSE]

How can I add rawCountTable into edgeR and tell it that the first column represet the y$genes?

Thank you in advance

Your gene names are already row names for rawCountTable, so there's no need to explicitly assign a data.frame to y$genes to represent this information. It's perfectly fine to leave y$genes empty if you don't have any extra gene-level annotation to add.