DOQTL (version 1.8.0)

parameter.update: Parameter updating in HMM

Description

Not intended for external use.

Usage

parameter.update.alleles(geno, b, pseudocounts, prsmth) parameter.update.intensity(data, params, prsmth, founder.means)

Arguments

geno

Data.frame containing allele calls.

b

Three dimensional numeric array containing emission probabilities.

pseudocounts

Three dimensional numeric array containing pseudocounts for updating.

prsmth

Three dimensional numeric array containing posterior genotype probabilities.

data

A list with named elements containing the information needed to reconstruct genomes. When method = intensity: x: Numeric matrix, num.samples x num.snps, with X intensities for all samples. Sample IDs and SNP IDs must be in rownames and colnames. y: Numeric matrix, num.samples x num.snps, with Y intensities for all samples. Sample IDs and SNP IDs must be in rownames and colnames. sex: Character vector, containing "M" or F indicating sex. Sample IDs must be in names. gen: Character matrix containing the generation of DO outbreeding for each sample. FALSEor the DO, this should be "DO" followed by a number with no space between them. FALSEor CC mice, this should be CC. Sample IDs must be in names.

params

List containing two elements: r.t.means: three dimensional numeric array containing the genotype cluster means at each marker. r.t.covars: three dimensional numeric array containing the genotype cluster variances at each marker.

founder.means

Numeric matrix containing the founder intensity means for each marker.