R/allEndpoints.R
get_gene_differential_expression_values.RdRetrieve the differential expression results for a given gene among datasets matching the provided query and filter
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)
)An ensembl gene identifier which typically starts with ensg or an ncbi gene identifier or an official gene symbol approved by hgnc
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~").
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
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 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")
number
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 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
# 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"))
#> result.ID contrast.ID experiment.ID pvalue correctedPValue rank
#> <int> <char> <int> <num> <num> <num>
#> 1: 565737 118 18 0.4213 0.8083 0.5213
#> 2: 560596 135393 134 0.5214 0.9999 0.4142
#> 3: 560598 1060 134 0.0450 0.5422 0.0829
#> 4: 560599 1060 134 0.1648 0.9985 0.1480
#> 5: 560738 15628 233 0.1751 0.4526 0.3869
#> 6: 560738 15629 233 0.1751 0.4526 0.3869
#> factor.coefficient factor.logfc factor.pvalue baseline.ID
#> <num> <num> <num> <char>
#> 1: -0.1185 -0.1185 0.4213 119
#> 2: -0.2146 -0.2146 0.5300 135392
#> 3: 0.4842 0.4842 0.2025 1059
#> 4: 0.4842 0.4842 0.1648 1059
#> 5: -0.1005 -0.1005 0.6375 117789
#> 6: 0.2426 0.2426 0.1294 117789