parameter.update: Parameter updating in HMM

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

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.

Author(s)

Daniel Gatti

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.