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.