searchReadGroupSets: searchReadGroupSets function

Description Usage Arguments Details Value See Also Examples

View source: R/searchReadGroupSets.R

Description

Search for read group sets (sequence alignement, e.g BAM files).

Usage

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searchReadGroupSets(host, datasetId, name = NA_character_,
  biosampleId = NA_character_, nrows = Inf, responseSize = NA_integer_)

Arguments

host

URL of GA4GH API data server.

datasetId

The dataset to search.

name

Only return read group sets with this name (case-sensitive, exact match).

biosampleId

Specifying the id of a BioSample record will return only readgroups with the given biosampleId.

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/readgroupsets/search

Value

DataFrame object.

See Also

DataFrame, getReadGroupSet

Examples

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

## End(Not run)

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