stack1kg: couple together a group of VCFs

In ldblock: data structures for linkage disequilibrium measures in populations

Description

couple together a group of VCFs

Usage

stack1kg(chrs = as.character(1:22), index = FALSE, useEBI = TRUE)

Arguments

chrs	a vector of chromosome names for extraction from 1000 genomes VCF collection
index	logical telling whether VcfStack should attempt to create the local index; for 1000 genomes, the tbi are in the cloud and will be used by readVcf so FALSE is appropriate
useEBI	logical(1) defaults to TRUE ... use tabix-indexed vcf from EBI

Value

VcfStack instance

Note

The seqinfo component of returned stack will have NA for genome. Please set it manually; for useEBI=TRUE this would be GRCh38.

Examples

if (interactive()) {
  st1 = stack1kg()
  st1
  }

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