Noob question: replacing ensembl ID with the gene symbol?

Question

[cdeantoneo31]

I'm a noob with a very unclear idea of what I am doing, but I'm doing my best.

The other day, the ncbi webpage for downloading genomes and GTF files was down. As a result, I had to do my analysis on this RNA seq data using the ensembl files, which messed everything I know how to do up, and now my GSEA is in the ensemble ID (i.e., ENSMUSG00000000001) instead of a nice, clean, and easy to read gene ID (i.e., Gnai3)

Below is what I used to generate the GSEA

gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "ENSEMBL", 
             minGSSize = 3,
             scoreType = "pos",
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = "org.Mm.eg.db", 
             pAdjustMethod = "none")

I did try substituting the gene ID with the symbol using the second answer here, but got the following error

ensembl.genes <- (gene_list)
gene_list
ENSMUSG00000026166 ENSMUSG00000027514 ENSMUSG00000026582 ENSMUSG00000024401 ENSMUSG00000018916 
         8.3426962          8.2544408          8.1768632          7.7641708          7.6248835 
ENSMUSG00000078365 ENSMUSG00000040026 ENSMUSG00000058427 ENSMUSG00000107750 ENSMUSG00000028287 
         7.0340698          6.6905516          6.4591807          6.2520667          6.1017208 
ENSMUSG00000029380 ENSMUSG00000063171 ENSMUSG00000050587 ENSMUSG00000118159 ENSMUSG00000071341 
         5.5614790          5.5298819          4.9374363          4.7380874          4.5747161  ...
 [ reached getOption("max.print") -- omitted 2013 entries ]
geneIDs1 <- ensembldb::select(EnsDb.Mmusculus.v79, keys= ensembl.genes, keytype = "GENEID", columns = c("SYMBOL", "GENEID"))
Error in .select(x = x, keys = keys, columns = columns, keytype = keytype,  : 
  Argument keys should be a character vector, an object extending AnnotationFilter, a filter expression or an AnnotationFilterList.

Answer 1

[GenoMax]

See Kevin Blighe answer on how to use biomaRt : Question: Convert Ensembl Transcript Ids Ensmust To Gene Symbol In R

[cdeantoneo31]

this seems to only work for a couple of selected genes? I would like to replace all of the ensembl ID's in my GSE, as well as within my DEseq data, with the gene symbol

[Kevin Blighe]

There will always be genes that do not map between different annotations. It would help that you paste some here so that we can advise further.

In my answer in the other thread, to generate a complete biomaRt table for all genes, you can use this:

library(biomaRt)
mart <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')
annotTable <- getBM(
  attributes = c(
    'ensembl_gene_id',
    'mgi_symbol'),
  mart = mart)

The other command, for org.Mm.eg.db, functions in the same way as the package that you are using, i.e., EnsDb.Mmusculus.v79

[cdeantoneo31]

this worked exactly as I needed it too. Like you said, not all of the genes were replaced exactly, but the ones relevant to my needs were. Thank you so much