dEploid {DEploid} | R Documentation |
Deconvolute mixed haplotypes
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)