searchFeatures: searchFeatures function

Description Usage Arguments Details Value References See Also Examples

View source: R/searchFeatures.R

Description

Search for features (lines of genomic feature files).

Usage

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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

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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)

labbcb/GA4GHclient documentation built on Nov. 22, 2017, 2:19 p.m.