searchReadGroupSets: searchReadGroupSets function

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

Description

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

Usage

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

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

## End(Not run)

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