EB_for_wsaf: Perform Empirical Bayes Shrinkage, Loci-by-Loci

In IDEELResearch/vcfRmanip: Basic functions for manipulating VCFs within the VCFR object/R environment

Description

Perform Empirical Bayes Shrinkage, Loci-by-Loci

Usage

EB_for_wsaf(vcfRobj, imputemissing = T, seed = 48)

Arguments

imputemissing	boolean; Should imputation for missing loci be performed, if so take the mean of the loci function via the beta distribution
seed	numeric; global seed to be called before bayes shrinkage
vcfRobject	vcfR; a vcfR object

Details

Loci must all be biallelic. Imputation for missing loci is performed by drawing a random number from the beta-binomial model

Note, optim will fail

Value

matrix of wsaf (non-referent alelle) shrunk by a beta-binomial empirical bayes model

IDEELResearch/vcfRmanip documentation built on Nov. 17, 2020, 9:32 p.m.