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convenience function to merge get_gene_differential_expression_values…
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… and the taxon specified version
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@oganm
oganm committed Dec 11, 2024
1 parent c08c8d0 commit 63c6e84
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Showing 3 changed files with 289 additions and 69 deletions.
244 changes: 178 additions & 66 deletions R/allEndpoints.R
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Original file line number Diff line number Diff line change
Expand Up @@ -135,13 +135,14 @@ mem.getResultSets <- function(resultSet = NA_character_, raw = getOption(
#' get_result_sets(dataset = 1)
#' # get all contrasts comparing disease states. use filter_properties to see avaialble options
#' get_result_sets(filter = "baselineGroup.characteristics.value = disease")
get_result_sets <- function(datasets = NA_character_, resultSets = NA_character_,
filter = NA_character_, offset = 0, limit = 20, sort = "+id",
raw = getOption("gemma.raw", FALSE), memoised = getOption(
"gemma.memoised",
FALSE
), file = getOption("gemma.file", NA_character_),
overwrite = getOption("gemma.overwrite", FALSE)) {
get_result_sets <- function(
datasets = NA_character_, resultSets = NA_character_,
filter = NA_character_, offset = 0, limit = 20, sort = "+id",
raw = getOption("gemma.raw", FALSE), memoised = getOption(
"gemma.memoised",
FALSE
), file = getOption("gemma.file", NA_character_),
overwrite = getOption("gemma.overwrite", FALSE)) {
compressibles <- "filter"
open_api_name <- "get_result_sets"
internal <- FALSE
Expand Down Expand Up @@ -608,12 +609,13 @@ memget_dataset_differential_expression_analyses <- function(dataset, raw = getOp
#'
#' @examples
#' get_dataset_expression_for_genes("GSE2018", genes = c(10225, 2841))
get_dataset_expression_for_genes <- function(datasets, genes, keepNonSpecific = FALSE, consolidate = NA_character_,
raw = getOption("gemma.raw", FALSE), memoised = getOption(
"gemma.memoised",
FALSE
), file = getOption("gemma.file", NA_character_),
overwrite = getOption("gemma.overwrite", FALSE)) {
get_dataset_expression_for_genes <- function(
datasets, genes, keepNonSpecific = FALSE, consolidate = NA_character_,
raw = getOption("gemma.raw", FALSE), memoised = getOption(
"gemma.memoised",
FALSE
), file = getOption("gemma.file", NA_character_),
overwrite = getOption("gemma.overwrite", FALSE)) {
compressibles <- NULL
open_api_name <- "get_datasets_expression_levels_for_genes"
internal <- FALSE
Expand Down Expand Up @@ -1219,13 +1221,14 @@ memget_dataset_samples <- function(dataset, raw = getOption("gemma.raw", FALSE),
#' # filter below is equivalent to the call above
#' get_datasets(filter = "taxon.commonName in (mouse,human) and allCharacteristics.valueUri = http://purl.obolibrary.org/obo/UBERON_0002048")
#' get_datasets(query = "lung")
get_datasets <- function(query = NA_character_, filter = NA_character_, taxa = NA_character_,
uris = 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)) {
get_datasets <- function(
query = NA_character_, filter = NA_character_, taxa = NA_character_,
uris = 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)) {
compressibles <- "filter"
open_api_name <- "get_datasets"
internal <- FALSE
Expand Down Expand Up @@ -1333,13 +1336,14 @@ memget_datasets <- function(
#' @examples
#' get_datasets_by_ids("GSE2018")
#' get_datasets_by_ids(c("GSE2018", "GSE2872"))
get_datasets_by_ids <- function(datasets = NA_character_, filter = NA_character_, taxa = NA_character_,
uris = 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)) {
get_datasets_by_ids <- function(
datasets = NA_character_, filter = NA_character_, taxa = NA_character_,
uris = 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)) {
compressibles <- "filter"
open_api_name <- "get_datasets_by_ids"
internal <- FALSE
Expand Down Expand Up @@ -1437,28 +1441,27 @@ memget_datasets_by_ids <- function(
#' filename.
#'
#' @inherit processDifferentialExpressionAnalysisResultByGeneValueObject_tsv return
#' @export
#'
#' @keywords gene
#' @keywords internal
#'
#' @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"))
get_gene_differential_expression_values <- function(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)) {
.get_gene_differential_expression_values <- function(
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)) {
compressibles <- "filter"
open_api_name <- "get_datasets_differential_expression_analysis_results_for_gene"
internal <- FALSE
internal <- TRUE
keyword <- "gene"
header <- "text/tab-separated-values"
isFile <- TRUE
fname <- "get_gene_differential_expression_values"
fname <- ".get_gene_differential_expression_values"
preprocessor <- processDifferentialExpressionAnalysisResultByGeneValueObject_tsv
validators <- list(
gene = validateSingleID, query = validateOptionalQuery,
Expand All @@ -1471,13 +1474,13 @@ get_gene_differential_expression_values <- function(gene, query = NA_character_,
}
if ("character" %in% class(gemmaCache()) && gemmaCache() ==
"cache_in_memory") {
return(mem_in_memory_cache("get_gene_differential_expression_values",
return(mem_in_memory_cache(".get_gene_differential_expression_values",
gene = gene, query = query, taxa = taxa, uris = uris,
filter = filter, threshold = threshold, raw = raw,
memoised = FALSE, file = file, overwrite = overwrite
))
} else {
out <- memget_gene_differential_expression_values(
out <- mem.get_gene_differential_expression_values(
gene = gene,
query = query, taxa = taxa, uris = uris, filter = filter,
threshold = threshold, raw = raw, memoised = FALSE,
Expand All @@ -1494,17 +1497,18 @@ get_gene_differential_expression_values <- function(gene, query = NA_character_,
)
}

#' Memoise get_gene_differential_expression_values
#' Memoise .get_gene_differential_expression_values
#'
#' @noRd
memget_gene_differential_expression_values <- function(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)) {
mem_call <- memoise::memoise(get_gene_differential_expression_values,
mem.get_gene_differential_expression_values <- function(
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)) {
mem_call <- memoise::memoise(.get_gene_differential_expression_values,
cache = gemmaCache()
)
mem_call(
Expand All @@ -1514,6 +1518,112 @@ memget_gene_differential_expression_values <- function(gene, query = NA_characte
)
}

#' Retrieve the differential expression results for a given gene and taxa among datasets matching the provided query and filter
#'
#'
#'
#' @param gene An ensembl gene identifier which typically starts with ensg or an ncbi gene identifier or an official gene symbol approved by hgnc
#' @param 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~").
#' @param taxon A numerical taxon identifier or an ncbi taxon identifier or a taxon identifier that matches either its scientific or common name
#' @param 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 \code{allCharacteristics.valueUri}
#' @param filter Filter results by matching expression. Use \code{\link{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")
#' @param threshold number
#' @param raw \code{TRUE} to receive results as-is from Gemma, or \code{FALSE} to enable
#' parsing. Raw results usually contain additional fields and flags that are
#' omitted in the parsed results.
#' @param 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 \code{options(gemma.memoised = TRUE)} will ensure that the cache is always
#' used. Use \code{\link{forget_gemma_memoised}} to clear the cache.
#' @param file The name of a file to save the results to, or \code{NULL} to not write
#' results to a file. If \code{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.
#' @param overwrite Whether or not to overwrite if a file exists at the specified
#' filename.
#'
#' @return Varies
#' @keywords internal
#'
#' @examples
.get_gene_differential_expression_values_in_taxon <- function(
gene, query = NA_character_, taxon = 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)) {
compressibles <- "filter"
open_api_name <- "get_datasets_differential_expression_analysis_results_for_gene_in_taxon"
internal <- TRUE
keyword <- "gene"
header <- "text/tab-separated-values"
isFile <- TRUE
fname <- ".get_gene_differential_expression_values_in_taxon"
preprocessor <- processDifferentialExpressionAnalysisResultByGeneValueObject_tsv
validators <- list(
gene = validateSingleID, query = validateOptionalQuery,
filter = validateFilter, taxon = validateTaxon, threshold = validateNumber
)
endpoint <- "datasets/analyses/differential/results/taxa/{encode(taxon)}/genes/{encode(gene)}?&query={encode(query)}&filter={encode(filter)}&threshold={encode(threshold)}"
if (memoised) {
if (!is.na(file)) {
warning("Saving to files is not supported with memoisation.")
}
if ("character" %in% class(gemmaCache()) && gemmaCache() ==
"cache_in_memory") {
return(mem_in_memory_cache(".get_gene_differential_expression_values_in_taxon",
gene = gene, query = query, taxon = taxon, uris = uris,
filter = filter, threshold = threshold, raw = raw,
memoised = FALSE, file = file, overwrite = overwrite
))
} else {
out <- mem.get_gene_differential_expression_values_in_taxon(
gene = gene,
query = query, taxon = taxon, uris = uris, filter = filter,
threshold = threshold, raw = raw, memoised = FALSE,
file = file, overwrite = overwrite
)
return(out)
}
}
.body(
fname = fname, validators = validators, endpoint = endpoint,
envWhere = environment(), isFile = isFile, header = header,
raw = raw, overwrite = overwrite, file = file, attributes = TRUE,
open_api_name = open_api_name, .call = match.call()
)
}

#' Memoise .get_gene_differential_expression_values_in_taxon
#'
#' @noRd
mem.get_gene_differential_expression_values_in_taxon <- function(
gene, query = NA_character_, taxon = 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)) {
mem_call <- memoise::memoise(.get_gene_differential_expression_values_in_taxon,
cache = gemmaCache()
)
mem_call(
gene = gene, query = query, taxon = taxon, uris = uris,
filter = filter, threshold = threshold, raw = raw, memoised = FALSE,
file = file, overwrite = overwrite
)
}

#' Retrieve the GO terms associated to a gene
#'
#'
Expand Down Expand Up @@ -2118,13 +2228,14 @@ memget_platform_element_genes <- function(platform, probe, offset = 0L, limit =
#' @examples
#' get_platforms_by_ids("GPL1355")
#' get_platforms_by_ids(c("GPL1355", "GPL96"))
get_platforms_by_ids <- function(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)) {
get_platforms_by_ids <- function(
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)) {
compressibles <- "filter"
open_api_name <- "get_platforms_by_ids"
internal <- FALSE
Expand Down Expand Up @@ -2223,15 +2334,16 @@ memget_platforms_by_ids <- function(
#'
#' @examples
#' search_gemma("bipolar")
search_gemma <- function(query, taxon = NA_character_, platform = NA_character_,
limit = 100, resultType = "experiment", raw = getOption(
"gemma.raw",
FALSE
), memoised = getOption("gemma.memoised", FALSE),
file = getOption("gemma.file", NA_character_), overwrite = getOption(
"gemma.overwrite",
FALSE
)) {
search_gemma <- function(
query, taxon = NA_character_, platform = NA_character_,
limit = 100, resultType = "experiment", raw = getOption(
"gemma.raw",
FALSE
), memoised = getOption("gemma.memoised", FALSE),
file = getOption("gemma.file", NA_character_), overwrite = getOption(
"gemma.overwrite",
FALSE
)) {
compressibles <- NULL
open_api_name <- "search"
internal <- FALSE
Expand Down
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