allDatasets: All datasets

In oganm/gemmaAPI: A wrapper for Gemma's restful API

All datasets

Description

Lists all datasets, or datasets with provided identifiers

Usage

allDatasets(
  datasets = NULL,
  filter = NULL,
  offset = 0,
  limit = 20,
  sort = "+id",
  file = NULL,
  return = TRUE,
  overwrite = FALSE,
  memoised = FALSE
)

Arguments

datasets	Character vector of identifiers. Identifiers can either be the ExpressionExperiment ID or its short name (e.g. GSE1234). Retrieval by ID is more efficient. Only datasets that user has access to will be available. Do not combine different identifiers in one query.
filter	Filtering can be done on any* property of a supported type or nested property that the ExpressionExperiment class has ( and is mapped by hibernate ). E.g: 'curationDetails' or 'curationDetails.lastTroubledEvent.date' Currently supported types are: String - property of String type, required value can be any String. Number - any Number implementation. Required value must be a string parseable to the specific Number type. Boolean - required value will be parsed to true only if the string matches 'true', ignoring case. Accepted operator keywords are: '=' - equality '!=' - non-equality '<' - smaller than '=>' - larger or equal 'like' similar string, effectively means 'contains', translates to the sql 'LIKE' operator (given value will be surrounded by Multiple filters can be chained using 'AND' or 'OR' keywords. Leave space between the keywords and the previous/next word! E.g: ?filter=property1 < value1 AND property2 like value2 If chained filters are mixed conjunctions and disjunctions, the query must be in conjunctive normal form (CNF). Parentheses are not necessary - every AND keyword separates blocks of disjunctions. Example: ?filter=p1 = v1 OR p1 != v2 AND p2 <= v2 AND p3 > v3 OR p3 < v4 Above query will translate to: (p1 = v1 OR p1 != v2) AND (p2 <= v2) AND (p3 > v3 OR p3 < v4;) Breaking the CNF results in an error. Filter "curationDetails.troubled" will be ignored if user is not an administrator.
offset	Integer. Optional parameter (defaults to 0) skips the specified amount of datasets when retrieving them from the database.
limit	Integer. Optional parameter (defaults to 20) limits the result to specified amount of datasets. Use 0 for no limit.
sort	Character. Optional parameter (defaults to +id) sets the ordering property and direction. Format is [+,-][property name]. E.g. "-accession" will translate to descending ordering by the Accession property. Note that this does not guarantee the order of the returned entities. Nested properties are also supported (recursively). E.g: +curationDetails.lastTroubledEvent.date
file	Character. File path. If provided, response will be saved to file
return	Logical. If the response should be returned. Set to false when you only want to save a file
overwrite	Logical. If TRUE, existing files will be overwritten. If FALSE a warning will be thrown and no action is taken.
memoised	Logical. If TRUE a memoised version of the function will be used which is faster for repeated requests. Use forgetGemmaMemoised to clear memory.

Value

List of lists containing experiment object.

Examples

# only non-troubled datasets
allDatasets(filter ='curationDetails.troubled = false')

# return all datasets. it is slower and prone to connection interruptions
# alternative is to loop using offset and limit
## Not run: 
allDatasets(limit = 0)

## End(Not run)

oganm/gemmaAPI documentation built on July 23, 2022, 8:26 p.m.