searchReads: searchReads function

Description Usage Arguments Details Value References See Also Examples

View source: R/searchReads.R

Description

Search for reads by genomic range (bases of aligned sequences)

Usage

1
2
3
searchReads(host, readGroupIds, referenceId = NA_character_,
  start = NA_integer_, end = NA_integer_, nrows = Inf,
  responseSize = NA_integer_)

Arguments

host

URL of GA4GH API data server.

readGroupIds

The ReadGroups to search. At least one id must be specified.

referenceId

The reference to query. Leaving blank returns results from all references, including unmapped reads - this could be very large.

start

The start position (1-based) of this query. If a reference is specified, this 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, exclusive) of this query. If a reference is specified, this defaults to the reference's length.

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/reads/search.

Value

DataFrame object.

References

Official documentation.

See Also

DataFrame

Examples

1
2
3
4
5
6
7
8
host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
readGroupIds <- "WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5Il0"
referenceSetId <- searchReferenceSets(host, nrows = 1)$id
referenceId <- searchReferences(host, referenceSetId, nrows = 1)$id
searchReads(host, readGroupIds, referenceId, start = 15000, end = 16000)

## End(Not run)

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