s3_1kg: Create a URL referencing 1000 genomes content in AWS S3.

In ldblock: data structures for linkage disequilibrium measures in populations

Description

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

Usage

s3_1kg(
  chrnum,
  tag = "20130502",
  wrap = function(x) TabixFile(x),
  tmpl = NULL,
  dropchr = TRUE
)

Arguments

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

Value

by default, a TabixFile instance

Examples

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

ldblock documentation built on Nov. 8, 2020, 5:33 p.m.