I made a DGEList object.
d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$HGNC_symbol)
I added additional parameters to the list.
rownames(d) <- COUNTS$Ensembl d$ENTREZ <- COUNTS$NCBI_geneID d$ENSEMBL <- COUNTS$Ensembl d$Symbol <- COUNTS$HGNC_symbol d$length <- COUNTS$Length d$gc <- COUNTS$GC
Then I filtered the list.
keep <- rowSums(cpm(d)>2)>= 3 d <- d[keep,] dim(d)
The filtering worked on the original DGEList object but not on the added parameters.
13980 more rows ...
 7105 64102 8813 57147 55732
58228 more elements ...
 ENSG00000000003 ENSG00000000005 ENSG00000000419 ENSG00000000457 ENSG00000000460
58233 Levels: ENSG00000000003 ENSG00000000005 ENSG00000000419 ENSG00000000457 ... ENSG00000284600
58228 more elements etc.
I was wondering if there is a way to filter the added parameters as well to keep all the info in one place for downstream analysis.
Thank you for your help and time.