parameter.update {DOQTL} | R Documentation

## 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

[Package DOQTL version 1.16.2 Index]