Retrieve the platforms of a dataset
A numerical dataset identifier or a dataset short name
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.
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.
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.
Whether or not to overwrite if a file exists at the specified filename.
A data table with information about the platform(s). 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:
platform.ID: Internal identifier of the platform
platform.shortName: Shortname of the platform.
platform.name: Full name of the platform.
platform.description: Free text description of the platform
platform.troubled: Whether or not the platform was marked "troubled" by a Gemma process or a curator
platform.experimentCount: Number of experiments using the platform within Gemma
platform.type: Technology type for the platform.
taxon.name: Name of the species platform was made for
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 underyling database used in Gemma for the taxon
get_dataset_platforms("GSE2018")
#> platform.ID platform.shortName
#> <int> <char>
#> 1: 1 GPL96
#> platform.name
#> <char>
#> 1: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A
#> platform.description
#> <char>
#> 1: The U133 set includes 2 arrays with a total of 44928 entries and was indexed 29-Jan-2002. The set includes over 1,000,000 unique oligonucleotide features covering more than 39,000 transcript variants, which in turn represent greater than 33,000 of the best characterized human genes. Sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 133 of UniGene (April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases including the Washington University EST trace repository and the University of California, Santa Cruz golden-path human genome database (April 2001 release). In addition, ESTs were analyzed for untrimmed low-quality sequence information, correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation. Keywords = high density oligonucleotide array\nFrom GPL96\nLast Updated: Mar 09 2006
#> platform.troubled platform.experimentCount platform.type taxon.name
#> <lgcl> <int> <char> <char>
#> 1: FALSE 389 ONECOLOR human
#> taxon.scientific taxon.ID taxon.NCBI taxon.database.name taxon.database.ID
#> <char> <int> <int> <char> <int>
#> 1: Homo sapiens 1 9606 hg38 87