importHaplo {AlphaSimR}

Import haplotypes

Description

Formats haplotype in a matrix format to an AlphaSimR population that can be used to initialize a simulation. This function serves as wrapper for newMapPop that utilizes a more user friendly input format.

Usage

importHaplo(haplo, genMap, ploidy = 2L, ped = NULL)

Arguments

haplo

a matrix of haplotypes

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

ploidy

ploidy level of the organism

ped

an optional pedigree for the supplied genotypes. See details.

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.

Value

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

Examples

haplo = rbind(c(1,1,0,1,0),
              c(1,1,0,1,0),
              c(0,1,1,0,0),
              c(0,1,1,0,0))
colnames(haplo) = 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 = importHaplo(haplo=haplo, 
                         genMap=genMap,
                         ploidy=2L,
                         ped=ped)