Using queryMany() in mygene package: Problem of querying Entrez gene IDs based on UniGene IDs in rat.
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chaof • 0
@65b554a4
Last seen 6 weeks ago
United States

I am trying to get the list of entrez ids based on the unigene ids from rat. I used your queryMany() in the package of mygene.

However, it always gives me the error message of Error in rename(df, c(X_id = "_id")) : Some 'from' names in value not found on 'x': X_id

If my input is a symbol, it works perfectly fine. For example, I have two rat genes Abcc3 and Havcr1

xli <- c('Abcc3', 'Havcr1') queryMany(xli, scopes = "symbol", fields="entrezgene", species="rat") Finished DataFrame with 2 rows and 4 columns query _id X_score entrezgene <character> <character> <numeric> <character> 1 Abcc3 140668 62.3720 140668 2 Havcr1 286934 67.7964 286934

However, if I use unigene ids as input, I got the error.

unigenelist <-c (128323, 165430) unigenelist [1] 128323 165430 queryMany(unigenelist, scopes="unigene", fields="entrezgene", species="rat") Finished Error in rename(df, c(X_id = "_id")) : Some 'from' names in value not found on 'x': X_id

```

mygene queryMany • 105 views
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Guido Hooiveld ★ 3.3k
@guido-hooiveld-2020
Last seen 11 days ago
Wageningen University, Wageningen, the …

I am not familiar with the package mygene, but please note that unigene has been retired 3 years ago! https://ncbiinsights.ncbi.nlm.nih.gov/2019/07/30/the-unigene-web-pages-are-now-retired/ I don;t know how mygene is working under the hood, but this could be a reason you don't get any results. You could also wonder how up-to-date unigene mappings still are.

Yet, in your case its seem your unigene ids are not unigene ids, or they are not properly formatted. As far as I know, they always started with an abbreviated species name, such as Rn or Hs.

Using your code that I slightly modified:

> xli <- c('Abcc3', 'Havcr1')
> queryMany(xli, scopes = "symbol", fields=c("entrezgene", "unigene"), species="rat")
Finished
DataFrame with 2 rows and 5 columns
        query         _id   X_score  entrezgene     unigene
  <character> <character> <numeric> <character> <character>
1       Abcc3      140668   62.3798      140668    Rn.88248
2      Havcr1      286934   67.9144      286934    Rn.11154
>

You will see unigene ids are still returned.

When using these 2 unigene ids as input:

> unigenelist <- c("Rn.88248", "Rn.11154")
> queryMany(unigenelist, scopes="unigene", fields=c("entrezgene", "symbol"), species="rat")
Finished
DataFrame with 2 rows and 5 columns
        query         _id   X_score  entrezgene      symbol
  <character> <character> <numeric> <character> <character>
1    Rn.88248      140668   14.0418      140668       Abcc3
2    Rn.11154      286934   14.1912      286934      Havcr1

>

... it shows that unigene ids are still being mapped.

My conclusion: you are using as input some identifiers that are not unigene ids. Also, because of the retirement of unigene, I would make use of another id for annotating results.

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