Retrieve the physical locations of a given gene

Retrieve the physical locations of a given gene

get_gene_locations(
  gene,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

gene

An ensembl gene identifier which typically starts with ensg or an ncbi gene identifier or an official gene symbol approved by hgnc

raw

TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.

memoised

Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.

file

The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.

overwrite

Whether or not to overwrite if a file exists at the specified filename.

Value

A data table with information about the physical location of the queried gene. A list if raw = TRUE. A 404 error if the given identifier does not map to any object.

The fields of the output data.table are:

• chromosome: Name of the chromosome the gene is located

• strand: Which strand the gene is located

• nucleotide: Nucleotide number for the gene

• length: Gene length

• taxon.name: Name of the taxon

• taxon.scientific: Scientific name for the taxon

• taxon.ID: Internal ID for the taxon given by Gemma

• taxon.NCBI: NCBI ID for the taxon

• taxon.database.name: Name of the database used in Gemma for the taxon

Examples

get_gene_locations("DYRK1A")
#>    chromosome strand nucleotide length taxon.name  taxon.scientific taxon.ID
#>        <char> <char>      <int>  <int>     <char>            <char>    <int>
#> 1:         11      +   33890705 118714        rat Rattus norvegicus        3
#> 2:         21      +   37365572 160785      human      Homo sapiens        1
#> 3:         16      +   94370769 125608      mouse      Mus musculus        2
#>    taxon.NCBI taxon.database.name taxon.database.ID
#>         <int>              <char>             <int>
#> 1:      10116                 rn6                86
#> 2:       9606                hg38                87
#> 3:      10090                mm10                81
get_gene_locations(1859)
#>    chromosome strand nucleotide length taxon.name taxon.scientific taxon.ID
#>        <char> <char>      <int>  <int>     <char>           <char>    <int>
#> 1:         21      +   37365572 160785      human     Homo sapiens        1
#>    taxon.NCBI taxon.database.name taxon.database.ID
#>         <int>              <char>             <int>
#> 1:       9606                hg38                87