vs_read_vcf: Reading a VCF file

In variantspark: A 'Sparklyr' Extension for 'VariantSpark'

Description

The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. The vs_read_vcf() reads this format and returns a jobj object from VCFFeatureSource scala class.

Usage

vs_read_vcf(vsc, path)

Arguments

vsc	A variantspark connection.
path	The file's path.

Value

spark_jobj, shell_jobj

Examples

 
## Not run: 
library(sparklyr)

sc <- spark_connect(master = "local")
vsc <- vs_context(sc)

hipster_vcf <- vs_read_vcf(vsc, 
                           system.file("extdata/hipster.vcf.bz2",
                                       package = "variantspark"))

hipster_vcf 

## End(Not run)

variantspark documentation built on June 13, 2019, 5:03 p.m.