searchFeatures: searchFeatures function

In GA4GHclient: A Bioconductor package for accessing GA4GH API data servers

Description

Search for features (lines of genomic feature files).

Usage

searchFeatures(host, featureSetId, name = NA_character_,
  geneSymbol = NA_character_, parentId = NA_character_,
  referenceName = NA_character_, start = NA_integer_, end = NA_integer_,
  featureTypes = character(), nrows = Inf, responseSize = NA_integer_)

Arguments

host	URL of GA4GH API data server.
featureSetId	The annotation set to search within. Either featureSetId or parentId must be non-empty.
name	Only returns features with this name (case-sensitive, exact match).
geneSymbol	Only return features with matching the provided gene symbol (case-sensitive, exact match). This field may be replaced with a more generic representation in a future version.
parentId	Restricts the search to direct children of the given parent feature ID. Either feature_set_id or parent_id must be non-empty.
referenceName	Only return features on the reference with this name (matched to literal reference name as imported from the GFF3).
start	Required, if name or symbol not provided. The beginning of the window (0-based, inclusive) for which overlapping features should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).
end	Required, if name or symbol not provided. The end of the window (0-based, exclusive) for which overlapping features should be returned.
featureTypes	TODO: To be replaced with a fully featured ontology search once the Metadata definitions are rounded out. If specified, this query matches only annotations whose feature_type matches one of the provided ontology terms.
nrows	Number of rows of the data frame returned by this function. If not defined, the function will return all entries. If the number of available entries is less than the value of this this parameter, the function will silently return only the available entries.
responseSize	Specifies the number of entries to be returned by the server until reach the number of rows defined in nrows parameter or until get all available entries. If not defined, the server will return the allowed maximum reponse size. Increasing this the value of this parameter will reduce the number of requests and reducing the time required. The will not respect this parameter if the value if larger than its maximum response size.

Details

This function requests POST host/features/search.

Value

DataFrame object.

References

Official documentation.

See Also

DataFrame, getFeature

Examples

host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
datasetId <- searchDatasets(host, nrows = 1)$id
featureSetId <- searchFeatureSets(host, datasetId, nrows = 1)$id
searchFeatures(host, featureSetId, nrows = 10)

## End(Not run)

GA4GHclient documentation built on Nov. 8, 2020, 5:47 p.m.