searchFeatures: searchFeatures function
In labbcb/GA4GHclient: A Bioconductor package for accessing GA4GH API data servers

Description Usage Arguments Details Value References See Also Examples

Search for features (lines of genomic feature files).

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_)

`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.

This function requests POST host/features/search.

DataFrame object.

Official documentation.

DataFrame, getFeature

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)