emission.probs.allele {DOQTL} | R Documentation

## Calculate the emission probabilities

### Description

Calculate the emission probabilities

### Usage

      emission.probs.allele(founders, chr, snps, sex = c("F", "M"))
      emission.probs.intensity(data, params)

### Arguments

`founders` | List containing founder information for non-DO or CC crosses. When method = allele: geno: Character matrix, num.samples x num.snps, with allele calls for all founders and FALSE1s (if available). 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. code: Character vector containing two letter genotype codes for each founder sample. Sample IDs must be in names.
`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.
`chr` | Character string containing the current chromosome.
`snps` | Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
`sex` | Character containing either FALSE or M, indicating the sex of the samples.
`params` | List containing two elements: r.t.means : Three dimensional array containing rho and theta genotype cluster means. r.t.covars : Three dimensional array containing rho and theta genotype cluster variances.

### Details

Given the founder allele calls or the rho and theta intensities, calculate the emission probabilities.

### Value

Three dimensional numeric array containing the emission probabilities for each sample at each marker.

### Author(s)

Daniel Gatti

### Examples

      ## Not run:  emission.probs.allele(founders, chr, snps, sex = c(F, "M"))

[Package DOQTL version 1.18.0 Index]