hmm: HMM function.
In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

hmm	R Documentation

HMM function.

Description

Not for external use.

Usage

  hmm.allele(data, founders, sex, snps, chr, trans.prob.fxn)
  hmm.intensity(data, founders, sex, snps, chr, trans.prob.fxn)

Arguments

`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. When method = allele: geno: Character matrix, num.samples x num.snps, with allele calls 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.
`founders`	List containing founder information for non-DO or CC crosses. Not required for DO. When method = intensity: x: Numeric matrix, num.samples x num.snps, with X intensities for all founders and FALSE1s (if available). Sample IDs and SNP IDs must be in rownames and colnames. y: Numeric matrix, num.samples x num.snps, with Y intensities 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. 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.
`sex`	Character that is either FALSE or M, indicating the sex of the animals. Only used on X chromosome.
`snps`	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
`chr`	Character indicating the current chromosome.
`trans.prob.fxn`	FALSEunction to use to determine the transition probability between markers.