hapSim: Generate Genotypic Data

Description

Simulate gametic data from a pedigree.

Usage

hapSim(ped,gmap,ids,hap,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", ... Note that 0 is reserved for missing values.

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 left of the chromosome. If gmap is missing but hap not, all but the first two columns of hap are ignored.

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, ids should be referred to "old" IDs.

hap

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 an individual, the haplotype should be (f1 m1 f2 m2 ...) where fi is the allele from father at the i-th locus and mi is the allele from mother at the i-th locus. Elements should be non-negative integers that are not larger than 16384. If missing, two founders with alleles 1 and 2 are assumed.

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

# NOT RUN {
data(miscEx)

# }
# NOT RUN {
# prepare pedigree in desired format
pedR<- pedRecode(pedF8)
# fake founder haplotypes
hapDat<- rbind(rep(1:2,nrow(gmapF8)),rep(3:4,nrow(gmapF8)))
# simulate hyplotypes for F8 individuals
hd<- hapSim(pedR, gmapF8, ids=pedR$id[pedR$gen=="F8"],
   hap=hapDat, recode.pedigree=TRUE)
dim(hd)
hd[1:5,1:10]
# }