hmm: HMM function.

In DOQTL: Genotyping and QTL Mapping in DO Mice

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.

Author(s)

Daniel Gatti

DOQTL documentation built on May 6, 2019, 3:09 a.m.