AnnotateVcf-CellBaseR-method: AnnotateVcf

In melsiddieg/cellbaseR: Querying annotation data from the high performance Cellbase web

AnnotateVcf

Description

This method is a convience method to annotate bgzipped tabix-indexed vcf files. It should be ideal for annotating small to medium sized vcf files.

Usage

## S4 method for signature 'CellBaseR'
AnnotateVcf(object, file, batch_size, num_threads, BPPARAM = bpparam())

Arguments

object	an object of class CellBaseR
file	Path to a bgzipped and tabix indexed vcf file
batch_size	intger if multiple queries are raised by a single method call, e.g. getting annotation info for several genes, queries will be sent to the server in batches. This slot indicates the size of each batch, e.g. 200
num_threads	number of asynchronus batches to be sent to the server
BPPARAM	a BiocParallel class object

Value

a dataframe with the results of the query

See Also

https://github.com/opencb/cellbase/wiki and the RESTful API documentation http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/

Examples

cb <- CellBaseR()
fl <- system.file("extdata", "hapmap_exome_chr22_200.vcf.gz",
                  package = "cellbaseR" )
res <- AnnotateVcf(object=cb, file=fl, BPPARAM = bpparam(workers=2),batch_size=100)

melsiddieg/cellbaseR documentation built on Jan. 16, 2024, 4:12 a.m.