subGprobs {hoardeR}

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