get_platforms_by_ids: Retrieve all platforms matching a set of platform identifiers

In PavlidisLab/Gemma-API: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Retrieve all platforms matching a set of platform identifiers

Description

Retrieve all platforms matching a set of platform identifiers

Usage

get_platforms_by_ids(
  platforms = NA_character_,
  filter = NA_character_,
  taxa = NA_character_,
  offset = 0L,
  limit = 20L,
  sort = "+id",
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

platforms	Platform numerical identifiers or platform short names. If not specified, all platforms will be returned instead
filter	Filter results by matching expression. Use filter_properties function to get a list of all available parameters. These properties can be combined using "and" "or" clauses and may contain common operators such as "=", "<" or "in". (e.g. "taxon.commonName = human", "taxon.commonName in (human,mouse), "id < 1000")
taxa	A vector of taxon common names (e.g. human, mouse, rat). Providing multiple species will return results for all species. These are appended to the filter and equivalent to filtering for taxon.commonName property
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.
sort	Order results by the given property and direction. The '+' sign indicate ascending order whereas the '-' indicate descending.
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 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

Examples

get_platforms_by_ids("GPL1355")
get_platforms_by_ids(c("GPL1355", "GPL96"))

PavlidisLab/Gemma-API documentation built on Dec. 15, 2024, 12:45 a.m.