Variants: Methods for accessing varinant data

In BaseSpaceR: R SDK for BaseSpace RESTful API

Description

Manipulating variant data.

Usage

getVariantSet(x, ...)
getVariants(x, ...)

Arguments

x	An object of class AppAuth.
...	Adiditional arguments supported by the REST API. id File id (for a BAM file) within BaseSpace. chrom Character string given the chromosome name (UCSC).

Details

Coming soon...

Value

These methods return a list with a representation of variant data.

Author(s)

Adrian Alexa

References

https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

See Also

AppAuth.

Examples

data(aAuth)

## get the ids of VCF files (within an AppResult? )
reseq <- listAppResults(aAuth, projectId = 21383369, Limit = 1)
AppResults(reseq)

vcfs <- listFiles(AppResults(reseq), Extensions = ".vcf")
Name(vcfs)
Id(vcfs)
vcfs

## Not run: 
## variant metadata
getVariantSet(aAuth, vid)

## get the variants
getVariants(aAuth, vid, chrom = "chr")

v <- getVariants(aAuth, vid, chrom = "chr", EndPos = 1000000L, Limit = 5)
v

## End(Not run)

BaseSpaceR documentation built on Nov. 8, 2020, 5:12 p.m.