hapSim: Generate Genotypic Data

Description

Simulate gametic data from a pedigree.

Usage

hapSim(ped,gmap,ids,hap.data,method=c("Haldane","Kosambi"),
   recode.pedigree=FALSE)

Arguments

ped

a pedigree, which is a data frame (id, sex, sire, dam, ...). In "sex", male should be "M", "Male" or 1, and female should be "F", "Female" or 2 (other than 0 and 1). If given, "generation" can be numeric 0, 1, 2, ... or non-numeric "F0", "F1", "F2", ... N

gmap

a genetic map. Should be data frame (snp, chr, dist, ...), where "snp" is the SNP (marker) name, "chr" is the chromosome where the "snp" is, and "dist" is the genetic distance in centi-Morgan (cM) from the leftmost SNP (marker) on the chromosome.

ids

genotypic data are extracted only for individuals with IDs specified by ids. If missing, genotypic data are extracted for all individuals in the pedigree. If ped is an object of pedRecode

hap.data

founders' haplotype data if not missing. Rows correspond to all founders, which should be in the first places in the pedigree ped, in the exact order and columns correspond to loci in the genetic map gmap in the exact order. For

method

whether "Haldane" or "Kosambi" mapping function should be used. This will be ignored if the recombination rate recRate is a component of gmap.

recode.pedigree

a logical variable. True if the pedigree needs to be recoded.

Value

a matrix giving haplotypes.

Details

The pedigree should be in the same format as an output of pedRecode.

Examples

Run this code

data(miscEx)

# prepare pedigree in desired format
pedR<- pedRecode(ped)
# fake founder haplotypes
hapDat<- rbind(rep(1:2,nrow(genMapF34)),rep(3:4,nrow(genMapF34)))
# simulate hyplotypes for F34 individuals
hd<- hapSim(pedR, genMapF34, ids=pedR$id[pedR$gen=="F34"],
   hap.data=hapDat, recode.pedigree=TRUE)
dim(hd)
hd[1:5,1:10]