s3_1kg {ldblock}R Documentation

Create a URL referencing 1000 genomes content in AWS S3

Description

Create a URL referencing 1000 genomes content in AWS S3.

Usage

s3_1kg(chrnum, tag = "20130502", wrap = function(x) TabixFile(x), tmpl = NULL, dropchr = TRUE)
stack1kg(chrs=as.character(1:22), index = FALSE)

Arguments

chrnum

a character string denoting a chromosome, such as '22'

chrs

a vector of chromosome names for extraction from 1000 genomes VCF collection

tag

a character string identifying the version, ignored if tmpl is non-null; valid tag values are the default or "20101123"

wrap

The URL is returned after evaluating wrap on it; default is useful when Tabix indexing is to be used

tmpl

alternate template for full URL, useful if versions prior to 2010 are of interest

dropchr

if TRUE chrnum will have 'chr' removed if present

index

a logical indicating if the vcf index files should be created (for stack1kg)

Details

stack1kg produces a VcfStack instance with references to VCF for 1000 genomes autosomal chrs. S3-resident VCF files with version "v5a.20130502" are used.

Value

by default, a TabixFile instance

Examples

s3_1kg("22")
## Not run: 
 require(VariantAnnotation)
 scanVcfHeader(s3_1kg("22"))
 
## End(Not run)

[Package ldblock version 1.12.1 Index]