listReferenceBases: listReferenceBases function

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

Description

Get the sequence bases of a reference genome by genomic range.

Usage

listReferenceBases(host, referenceId, start = 1, end = NA_integer_)

Arguments

host	URL of GA4GH API data server.
referenceId	The ID of the Reference to be retrieved.
start	The start position (1-based) of this query. Defaults to 0. 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 1).
end	The end position (1-based, inclusive) of this query. Defaults to the length of this Reference.

Details

This function requests POST host/listreferencebases.

Value

BString object.

See Also

searchReferenceSets, searchReferences

Examples

host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
referenceSetId <- searchReferenceSets(host, nrows = 1)$id
referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id
listReferenceBases(host, referenceId, start = 1, end = 100)

## End(Not run)

labbcb/GA4GHclient documentation built on May 20, 2019, 7:32 p.m.