subGprobs: Rewrite the Gprobs File from a Beagle Output

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

Rewrite the Gprobs File from a Beagle Output

Description

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

Usage

  subGprobs(file=NULL, vmmk=NULL, out=NULL, chunkSize=100000, removeInsertions=TRUE,
             verbose = TRUE, writeOut=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.
removeInsertions	All Indels will be removed.
verbose	The function gives feedback.
writeOut	Logical, write the output back to the HDD.

Details

This function takes a Beagle Gprobs 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 Gprobs file.

Author(s)

Daniel Fischer

fischuu/hoardeR documentation built on April 13, 2024, 1:20 p.m.