get_platform_annotations: Retrieve Platform Annotations by Gemma

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

Retrieve Platform Annotations by Gemma

Description

Gets Gemma's platform annotations including mappings of microarray probes to genes.

Usage

get_platform_annotations(
  platform,
  annotType = c("noParents", "allParents", "bioProcess"),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE),
  memoised = getOption("gemma.memoise", FALSE),
  unzip = FALSE
)

Arguments

platform	A platform numerical identifiers or platform short name.
annotType	Which GO terms should the output include
file	Where to save the annotation file to, or empty to just load into memory
overwrite	Whether or not to overwrite an existing file
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.
unzip	Whether or not to unzip the file (if @param file is not empty)

Value

A table of annotations

• ElementName: Probeset names provided by the platform. Gene symbols for generic annotations typicall used for RNA-seq experiments.

• GeneSymbols: Genes that were found to be aligned to the probe sequence. Note that it is possible for probes to be non-specific. Alignment to multiple genes are indicated with gene symbols separated by "|"s

• GeneNames: Name of the gene

• GOTerms: GO Terms associated with the genes. annotType argument can be used to choose which terms should be included.

• GemmaIDs and NCBIids: respective IDs for the genes.

Examples

head(get_platform_annotations("GPL96"))
head(get_platform_annotations('Generic_human_ncbiIds'))

jsicherman/GemmAPI documentation built on Dec. 15, 2024, 8:59 a.m.