genoSim: Generate Genotypic Data

Description

Simulate genotypic data from a pedigree in advanced intercross lines (AIL).

Usage

genoSim(ped, gmap, ids, hap, method = c("Haldane", "Kosambi"))

Value

A matrix, with entry value s-1 where s is the summation of the numbers representing two alleles at a locus. For instance, 1, 2, and 3 representing genotypes "AA", "AB" and "BB" respectively if hap is not specified. Each row represent an observation, and each column corresponds to SNP in gmap.

Arguments

ped: A pedigree, which is a data frame (id, sex, father/sire, mother/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", ..., which should be in an increasing order. Note that 0 is reserved for missing values. If a father/mother is an inbred founder, its ID should be tagged by character 'i' (e.g. 1i, 2i, etc.). See pedRecode.
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 founders as specified by row names, 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 hap is not supplied, founders are assumed to be inbred.
method: Whether "Haldane" or "Kosambi" mapping function should be used. This will be ignored if the recombination rate recRate is a component of gmap.

Details

The pedigree should be in the same format as an output of pedRecode. Sex chromosome should be marked by 'x' or 'X'. Founders mean those whose parents have 0 or negative IDs after the pedigree is recoded by pedRecode. In addition, it is assumed that there are not more than two founders; otherwise, you may run hapSim and then extract genotypes manually.

Examples

Run this code

data(miscEx)

if (FALSE) {
# simulate genotypes for F8 individuals
ids<- sapply(pedF8$id[pedF8$gen == "F8" & pedF8$sire != "32089"], as.character)
gdt<- genoSim(pedF8, gmapF8, ids=ids)
dim(gdt)
gdt[1:5,1:5]
}