vcfWindow: Read window from VCF
In CMWbio/weavR: weavR: Windowed Evolutionary Analysis and Visualisation in R.
Description
Usage
Arguments
Details
Value
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 May 26, 2019, 6:41 a.m.
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Description Usage Arguments Details Value
Description
Reads in a specified window from a tabix indexed Variant Call Format
Usage
1 | vcfWindow(fileName, contig, param, ploidy)
|
Arguments
fileName |
A |
contig |
A single element |
param |
An object of class |
ploidy |
|
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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