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.
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.
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
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)