vcfWindow: Read window from VCF

Description Usage Arguments Details Value

View source: R/readWindow.R

Description

Reads in a specified window from a tabix indexed Variant Call Format

Usage

1
vcfWindow(fileName, contig, param, ploidy)

Arguments

fileName

A character vector of length one containing the full path name for a Tabix indexed VCF

contig

A single element character vector containing the contig name in the VCF

param

An object of class ScanVcfParam containing a GRanges object for the target locus

ploidy

Integer or Numeric. The ploidy of the VCF, as called by Variant Caller

Details

Uses the package VariantAnnotation to read in a locus (window) from the target VCF,

Value

An object of class DNAbin from the package ape


CMWbio/weavR documentation built on March 19, 2018, 4:07 a.m.