searchCallSets: searchCallSets function

Description Usage Arguments Details Value See Also Examples

View source: R/searchCallSets.R

Description

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

Usage

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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

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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)

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