Import inbred, diploid genotypes

Formats the genotypes from inbred, diploid lines to an AlphaSimR population that can be used to initialize a simulation. An attempt is made to automatically detect 0,1,2 or -1,0,1 genotype coding. Heterozygotes or probabilistic genotypes are allowed, but will be coerced to the nearest homozygote. Pedigree information is optional and when provided will be passed to the population for easier identification in the simulation.

Usage

importInbredGeno(geno, genMap, ped = NULL)

Arguments

geno

a matrix of genotypes

genMap

genetic map as a data.frame. The first three columns must be: marker name, chromosome, and map position (Morgans). Marker name and chromosome are coerced using as.character. See importGenMap

ped

an optional pedigree for the supplied genotypes. See details.

Value

a MapPop-class if ped is NULL, otherwise a NamedMapPop-class

Details

The optional pedigree can be a data.frame, matrix or a vector. If the object is a data.frame or matrix, the first three columns must include information in the following order: id, mother, and father. All values are coerced using as.character. If the object is a vector, it is assumed to only include the id. In this case, the mother and father will be set to "0" for all individuals.

Examples

geno = rbind(c(2,2,0,2,0),
             c(0,2,2,0,0))
colnames(geno) = letters[1:5]

genMap = data.frame(markerName=letters[1:5],
                    chromosome=c(1,1,1,2,2),
                    position=c(0,0.5,1,0.15,0.4))

ped = data.frame(id=c("a","b"),
                 mother=c(0,0),
                 father=c(0,0))

founderPop = importInbredGeno(geno=geno,
                              genMap=genMap,
                              ped=ped)