AnnotateVcf,CellBaseR-method {cellbaseR} | R Documentation |
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.
## S4 method for signature 'CellBaseR' AnnotateVcf(object, file, batch_size, num_threads, BPPARAM = bpparam())
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 |
a dataframe with the results of the query
https://github.com/opencb/cellbase/wiki and the RESTful API documentation http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/
cb <- CellBaseR() fl <- system.file("extdata", "hapmap_exome_chr22_500.vcf.gz", package = "cellbaseR" ) res <- AnnotateVcf(object=cb, file=fl, BPPARAM = bpparam(workers=2))