Retrieve the genes associated to a probe in a given platform

Retrieve the genes associated to a probe in a given platform

get_platform_element_genes(
  platform,
  probe,
  offset = 0L,
  limit = 20L,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

platform

A platform numerical identifier or a platform short name

probe

A probe name or it's numerical identifier

offset

The offset of the first retrieved result.

limit

Defaults to 20. Limits the result to specified amount of objects. Has a maximum value of 100. Use together with offset and the totalElements attribute in the output to compile all data if needed.

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 querried gene(s) A list if raw = TRUE.

The fields of the output data.table are:

• gene.symbol: Symbol for the gene

• gene.ensembl: Ensembl ID for the gene

• gene.NCBI: NCBI id for the gene

• gene.name: Name of the gene

• gene.aliases: Gene aliases. Each row includes a vector

• gene.MFX.rank: Multifunctionality rank for the gene

• taxon.name: Name of the species

• taxon.scientific: Scientific name for the taxon

• taxon.ID: Internal identifier given to the species by Gemma

• taxon.NCBI: NCBI ID of the taxon

• taxon.database.name: Underlying database used in Gemma for the taxon

• taxon.database.ID: ID of the underlying database used in Gemma for the taxon

Examples

get_platform_element_genes("GPL1355", "AFFX_Rat_beta-actin_M_at")
#>    gene.symbol       gene.ensembl gene.NCBI   gene.name gene.aliases
#>         <char>             <char>     <int>      <char>       <list>
#> 1:        Actb ENSRNOG00000034254     81822 actin, beta         Actx
#>    gene.MFX.rank taxon.name  taxon.scientific taxon.ID taxon.NCBI
#>            <num>     <char>            <char>    <int>      <int>
#> 1:     0.9748069        rat Rattus norvegicus        3      10116
#>    taxon.database.name taxon.database.ID
#>                 <char>             <int>
#> 1:                 rn6                86