dEploid: Deconvolute mixed haplotypes

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Description

Deconvolute mixed haplotypes, and reporting the mixture proportions from each sample This function provieds an interface for calling dEploid from R. The command line options are passed via the args argument

Usage

dEploid(args)

Arguments

args	String of dEploid input.

Value

A list with members of haplotypes, proportions and log likelihood of the MCMC chain.

• Haps Haplotypes at the final iteration in plain text file.

• Proportions MCMC updates of the proportion estimates.

• llks Log likelihood of the MCMC chain.

Seeding

The R version of DEploid uses random number from R's random generator. Therefore, the '-seed' argument of the command line version will be ignored, and no seed is given in the output. Use the R function 'set.seed' prior to calling this function to ensure reproduciblity of results.

See Also

• vignette('dEploid-Arguments') for an overview of commandline arguments

Examples

## Not run: 
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
set.seed(1234)
PG0390.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))

## End(Not run)

DEploid documentation built on April 22, 2020, 1:04 a.m.