R: Generate Genotypic Data

genoSim {QTLRel} | R Documentation

## 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"))

### 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", ..., which should be in an increasing order. Note that 0 is reserved for missing values. If a sire/dam 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.

### 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`.

### Note

Sex may be used as a covariate if significance on x-chromosome is assessed by gene dropping through this function.

### See Also

`pedRecode` for more information.

### Examples

    data(miscEx)

    ## Not run:
    # 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]

    ## End(Not run)

[Package QTLRel version 1.0 Index]