gprofiler output ENSG to gene name

Question

I would like to ask if there is any tool or R script that translates Ensembl IDs to gene names in a gprofiler GO output. An example of this file is the following one:

Answer 1

This is usually done using AnnotationDbi in combination with the annotation database for human org.Hs.eg.db.

library(org.Hs.eg.db)
genes <- c("ENSG00000102055", "ENSG00000232605", "ENSG00000136828",
           "ENSG00000159197", "ENSG00000201394", "ENSG00000278580",
           "ENSG00000213440", "ENSG00000166816", "ENSG00000275895",
           "ENSG00000105723")
select(org.Hs.eg.db, genes, c("ENSEMBL", "ALIAS"), "ENSEMBL")

This returns:

           ENSEMBL     ALIAS
1  ENSG00000102055       I-4
2  ENSG00000102055  PPP1R2P9
3  ENSG00000102055   PPP1R2C
4  ENSG00000232605      <NA>
5  ENSG00000136828   RALGEF2
6  ENSG00000136828  RALGPS1A
7  ENSG00000136828   RALGPS1
8  ENSG00000159197     ATFB4
9  ENSG00000159197      LQT5
10 ENSG00000159197      LQT6
11 ENSG00000159197     MIRP1
12 ENSG00000159197     KCNE2
13 ENSG00000201394   RN5S140
14 ENSG00000201394 RNA5SP140
15 ENSG00000278580      <NA>
16 ENSG00000213440      <NA>
17 ENSG00000166816     DLACD
18 ENSG00000166816       DLD
19 ENSG00000166816      LDHD
20 ENSG00000275895   U2AF1L5
21 ENSG00000105723     GSK3A

If you want to apply a 1:1 mapping of gene IDs to common names, you can use the "SYMBOL" column. In a data.frame, you can do something like this:

ensembl_to_symbol <- function(e) {
  hits <- select(org.Hs.eg.db, e, "SYMBOL", "ENSEMBL")$SYMBOL
  # Gene IDs without symbols should just stay as IDs
  no_hit <- is.na(hits)
  hits[no_hit] <- e[no_hit]
  hits
}

recode_symbols <- function(s) {
  e <- ensembl_to_symbol(unlist(strsplit(s, split = ",")))
  paste(e, collapse = ",")
}

df <- data.frame(
  genes = c(paste(genes[1:5], collapse = ","),
            paste(genes[6:10], collapse = ",")
  )
)

df$genes <- sapply(df$genes, recode_symbols)

This isn't the most vectorized (fast) solution, but it's probably easier to understand this way.