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

Description Usage Arguments Value Examples

View source: R/s3_1kg.R

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

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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

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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.