<p>I am trying to convert a list of gene names into Ensembl IDs but I'm having a bit of trouble.</p>

<p>I've tried using the EnsDb.Hsapiens.v86 package but I always get LRG-ID values returned as well, even when using the GeneIdFilter "startsWith" thing.<br>
My code looks like this:</p>

<pre><code>targets &lt;- as.character(targetCSV[, 2])


targetEnsemble &lt;- ensembldb::select(
      EnsDb.Hsapiens.v86, 
      filter = GeneIdFilter("ENS", "startsWith"),
      keys = targets, 
      keytype = "SYMBOL", 
      columns = c("SYMBOL","GENEID"))
</code></pre>

<p>And for example I get back:</p>

<pre><code>    SYMBOL          GENEID
1     CYR61 ENSG00000142871
2      CTGF ENSG00000118523
3    AMOTL2 ENSG00000114019
4    ANKRD1 ENSG00000148677
5    ANKRD1         LRG_379
6    IGFBP3 ENSG00000146674
7        F3 ENSG00000117525
</code></pre>

<p>I also tried using org.Hs.eg.db package but get a different problem where some of my genes return NA.</p>

<p>My code:</p>

<pre><code>  mapIds(x = org.Hs.eg.db, 
     keys = targets, 
     "ENSEMBL", 
     "SYMBOL",
     fuzzy = TRUE,
     multiVals = first)
</code></pre>

<p>And this works on some but not all the genes for some reason.</p>

<pre><code>    $CYR61
[1] NA

$CTGF
[1] NA

$AMOTL2
[1] "ENSG00000114019"

$ANKRD1
[1] "ENSG00000148677"

$IGFBP3
[1] "ENSG00000146674"

$F3
[1] "ENSG00000117525"
</code></pre>

<p>If anyone can solve either of these problems that would be great, thanks in advance!</p>

CC BY-SA 4.0
2020-04-24T13:54:05.070Z
Have you considered just downloading a list of gene IDs and the associated gene names from Ensembl Biomart?
Devon Ryan
CC BY-SA 4.0
2020-04-24T14:08:11.130Z
Yeah but I wanted to be able to change out the genesets quickly and this just added another annoying step
Jack Henry
CC BY-SA 4.0
2020-04-24T14:21:09.763Z
There's an R package to allow fetching those programmatically from biomart.
Devon Ryan
<r><gene><ensembl>
How to map gene names to ensembl Ids in R
# How to map gene names to ensembl Ids in R

(Asked by: username_0 on 2020-04-24)

I am trying to convert a list of gene names into Ensembl IDs but I'm having a bit of trouble.
I've tried using the EnsDb.Hsapiens.v86 package but I always get LRG-ID values returned as well, even when using the GeneIdFilter "startsWith" thing.
My code looks like this:
targets <- as.character(targetCSV[, 2])


targetEnsemble <- ensembldb::select(
      EnsDb.Hsapiens.v86, 
      filter = GeneIdFilter("ENS", "startsWith"),
      keys = targets, 
      keytype = "SYMBOL", 
      columns = c("SYMBOL","GENEID"))

And for example I get back:
    SYMBOL          GENEID
1     CYR61 ENSG00000142871
2      CTGF ENSG00000118523
3    AMOTL2 ENSG00000114019
4    ANKRD1 ENSG00000148677
5    ANKRD1         LRG_379
6    IGFBP3 ENSG00000146674
7        F3 ENSG00000117525

I also tried using org.Hs.eg.db package but get a different problem where some of my genes return NA.
My code:
  mapIds(x = org.Hs.eg.db, 
     keys = targets, 
     "ENSEMBL", 
     "SYMBOL",
     fuzzy = TRUE,
     multiVals = first)

And this works on some but not all the genes for some reason.
    $CYR61
[1] NA

$CTGF
[1] NA

$AMOTL2
[1] "ENSG00000114019"

$ANKRD1
[1] "ENSG00000148677"

$IGFBP3
[1] "ENSG00000146674"

$F3
[1] "ENSG00000117525"

If anyone can solve either of these problems that would be great, thanks in advance!

**Tags:** r, gene, ensembl
> **Comments:**
> **username_1**: Have you considered just downloading a list of gene IDs and the associated gene names from Ensembl Biomart?  
> **username_0**: Yeah but I wanted to be able to change out the genesets quickly and this just added another annoying step  
> **username_1**: There's an R package to allow fetching those programmatically from biomart.  

---

## 0 answers

