Answers.Body: <p><em>Answer from @devon-ryan, converted from comment:</em></p>
  <p>Try a UCSC gene ID instead. For those genes they'd be: <code>uc001zni.3</code> (INO80), <code>uc002vaz.4</code> (INO80D), <code>uc004eup.4</code> or <code>uc004eun.4</code> (SMARCA1) and <code>uc001coj.2</code>, <code>uc010olq.2</code>, <code>uc010olr.2</code>, <code>uc001coi.2</code> or <code>uc001col.2</code> (NASP). You might have to omit the versions (the <code>.4</code> part, for example).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-04T04:21:12.437Z
Answers.LastActivityDate: 2021-07-04T04:21:12.437Z
Answers.UserDisplayName: gringer
Body: <p>I want to get coordinates of human genes from my list (consisting of hgnc genes id) using GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene R packages from Bioconductor.</p>
  
  <pre><code>library(TxDb.Hsapiens.UCSC.hg19.knownGene)
  txdb=(TxDb.Hsapiens.UCSC.hg19.knownGene)
  
  my_genes = c("INO80","NASP","INO80D","SMARCA1")
  
  select(txdb, keys = my_genes,
     columns=c("TXCHROM","TXSTART","TXEND","TXSTRAND"), 
     keytype="GENEID")
  </code></pre>
  
  <p>However, it doesn't' work because txdb doesn't take hgnc identifiers; how can it be solved? I couldn't find any appropriate keytype that will support hgnc and not sure how to match hgnc id I have and GENEID from txdb.</p>
  
Tags: <r><bioconductor><sequence-annotation>
Title: Get genomic coordinates using GenomicFeatures by HGNC gene names
ThreadText: # Get genomic coordinates using GenomicFeatures by HGNC gene names
  
  (Asked by: username_0 on 2018-09-07)
  
  I want to get coordinates of human genes from my list (consisting of hgnc genes id) using GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene R packages from Bioconductor.
  
  ```
  library(TxDb.Hsapiens.UCSC.hg19.knownGene)
  txdb=(TxDb.Hsapiens.UCSC.hg19.knownGene)
  
  my_genes = c("INO80","NASP","INO80D","SMARCA1")
  
  select(txdb, keys = my_genes,
     columns=c("TXCHROM","TXSTART","TXEND","TXSTRAND"), 
     keytype="GENEID")
  
  ```
  
  However, it doesn't' work because txdb doesn't take hgnc identifiers; how can it be solved? I couldn't find any appropriate keytype that will support hgnc and not sure how to match hgnc id I have and GENEID from txdb.
  
  **Tags:** r, bioconductor, sequence-annotation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-07-04. Score: 0
  
  *Answer from @devon-ryan, converted from comment:*
  
  Try a UCSC gene ID instead. For those genes they'd be: `uc001zni.3` (INO80), `uc002vaz.4` (INO80D), `uc004eup.4` or `uc004eun.4` (SMARCA1) and `uc001coj.2`, `uc010olq.2`, `uc010olr.2`, `uc001coi.2` or `uc001col.2` (NASP). You might have to omit the versions (the `.4` part, for example).
  
  
  ---
  
  