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.
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.