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]