emission.probs.allele: Calculate the emission probabilities
In DOQTL: Genotyping and QTL Mapping in DO Mice

Description Usage Arguments Details Value Author(s) Examples

Calculate the emission probabilities

1 2	emission.probs.allele(founders, chr, snps, sex = c("F", "M")) emission.probs.intensity(data, params)

`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.