get_gene_differential_expression_values: Retrieve the differential expression results for a given gene...

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

Retrieve the differential expression results for a given gene among datasets matching the provided query and filter

Description

Retrieve the differential expression results for a given gene among datasets matching the provided query and filter

Usage

get_gene_differential_expression_values(
  gene,
  query = NA_character_,
  taxa = NA_character_,
  uris = NA_character_,
  filter = NA_character_,
  threshold = 1,
  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
query	The search query. Queries can include plain text or ontology terms They also support conjunctions ("alpha AND beta"), disjunctions ("alpha OR beta") grouping ("(alpha OR beta) AND gamma"), prefixing ("alpha*"), wildcard characters ("BRCA?") and fuzzy matches ("alpha~").
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
uris	A vector of ontology term URIs. Providing multiple terms will return results containing any of the terms and their children. These are appended to the filter and equivalent to filtering for allCharacteristics.valueUri
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")
threshold	number
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 containing differential expression results. This table is stripped down some relevant information for speed of execution. Details about the contrasts can be accessesed via get_result_sets function

The fields of the output data.table are:

• result.ID: Result set ID of the differential expression analysis. May represent multiple factors in a single model.

• contrast.ID: Id of the specific contrast factor. Together with the result.ID they uniquely represent a given contrast.

• experiment.ID: Id of the source experiment

• factor.coefficient: Model coefficient calculated for the specific contrast factor

• factor.logfc: Log 2 fold change calculated for the specific contrast factor

• factor.pvalue: p values calculated for the specific contrast factor

Examples

# get all differential expression results for ENO2
# from datasets marked with the ontology term for brain
head(get_gene_differential_expression_values(2026, uris = "http://purl.obolibrary.org/obo/UBERON_0000955"))

PavlidisLab/gemma.R documentation built on July 12, 2024, 10:42 a.m.