listReferenceBases: listReferenceBases function

Description Usage Arguments Details Value See Also Examples

View source: R/listReferenceBases.R

Description

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

Usage

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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

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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.