polyqtlR (version 0.1.1)

maxL_IBD: Wrapper function to run estimate_IBD function over multiple error priors

Description

Function to run the estimate_IBD function over a range of possible error priors. The function returns a merged set of results that maximise the marginal likelihood per individual, i.e. allowing a per-individual error rate within the options provided in the errors argument.

Usage

maxL_IBD(errors = c(0.01, 0.05, 0.1, 0.2), ...)

Value

A list containing the following components:

maxL_IBD

A nested list as would have been returned by the estimate_IBD function, but composite across error priors to maximise the marginal likelihoods. Note that the $error values per linkage group are now the average error prior across the population per linkage group

MML

A 3d array of the maximal marginal likelihoods, per error prior. Dimensions are individuals, linkage groups, error priors.

error_per_ind

A matrix of the most likely genotyping error rates per individual (in rows) for each linkage group (in columns)

errors

The error priors used (i.e. the input vector is returned for later reference.)

Arguments

errors

Vector of offspring error priors to test (each between 0 and 1)

...

Arguments passed to estimate_IBD.

Examples

if (FALSE) {
data("phased_maplist.4x","SNP_dosages.4x")
maxL_IBD(phased_maplist=phased_maplist.4x,genotypes=SNP_dosages.4x,
ploidy=4,errors=c(0.01,0.02,0.05,0.1))
}