searchCallSets: searchCallSets function

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

Description

Search for call sets (sample columns of VCF files).

Usage

searchCallSets(host, variantSetId, name = NA_character_,
  biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)

Arguments

host	URL of GA4GH API data server.
variantSetId	The VariantSet to search.
name	Only return call sets with this name (case-sensitive, exact match).
biosampleId	Return only call sets generated from the provided BioSample ID.
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/callsets/search.

Value

DataFrame object.

See Also

DataFrame, getCallSet

Examples

host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
searchCallSets(host, variantSetId)

## End(Not run)

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