I have my RNA sequencing results output from DeSEQ2 and eager to generate some figures. I try to run the following command, only for it to tell me that the input does not match the required format, when I clearly see that it is not true. Please if anybody knows how to fix this bug, I would kindly appreciate your contribution in comment section further.
GO.params.bp <- GSEAGOHyperGParams(name="GOstats",
geneSetCollection=gene_annotations,
geneIds = ensembl_gene_ids,
universeGeneIds = NULL,
ontology = "BP",
pvalueCutoff = cutoff,
conditional = FALSE,
testDirection = "over")
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘geneIdType’ for signature ‘"character"’
str(ensembl_gene_ids)
chr [1:3] "ENSG00000100592" "ENSG00000101336" "ENSG00000134285"
class(ensembl_gene_ids)
[1] "character"