subPhased: Rewrite the Phased File from a Beagle Output

In hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

Description

This function takes a phased Beagle output and rewrites the output.

Usage

  subPhased(file=NULL, vmmk = NULL, out=NULL, chunkSize=100000, verbose=TRUE,
            removeInsertions=TRUE)

Arguments

file	Location of the original Beagle file (String).
vmmk	Location of the Variant Map Master key (String).
out	Name and location of the output file (String).
chunkSize	For large Beagle files, the chunk size.
verbose	The function gives feedback.
removeInsertions	All Indels will be removed.

Details

This function takes a Beagle phased file and rewrites the alleles from numerical to character, based on the information provided in a variant map master key. For larger files the function can process the rewriting in chunks in order to save memory.

Value

A rewritten beagle phased file.

Author(s)

Daniel Fischer

hoardeR documentation built on May 2, 2019, 5:15 a.m.