R: Derive genetic matrices

genMatrix {QTLRel} | R Documentation

## Derive genetic matrices

### Description

Derive genetic matrices from Jacquard condensed identity coefficients or genotypic data.

### Usage

    genMatrix(x)

### Arguments

`x` | An object of `cic` or `ibs`, or genotypic data in a matrix or a data frame with each row representing an observation and each column a marker locus and entry being "AA", "AB", "BB" (or 1, 2, 3) without missing genotypes.

### Value

`AA` | Additive genetic matrix.
`DD` | Dominance genetic matrix.
`AD,HH,MH` | Other three genetic matrices (see Abney et. al. 2000).
`ib` | Inbreeding coefficients.

### References

Abney, M., M. S. McPeek, and C. Ober (2000). Estimation of variance components of quantitative traits in inbred populations. Am. J. Hum. Genet. 141, 629-650.

### See Also

`cic`

### Examples

    data(miscEx)

    ids<- sample(pedF8$id[300:500],20)

    ## Not run:
    # get condensed identity coefficients
    oo<- cic(pedF8, ids=ids, df=0)
    ksp<- kinship(pedF8, ids=ids) # kinship coefficients only
    # extract genetic matrices
    gm<- genMatrix(oo)
    sum((gm$AA-2*ksp)>1e-7) # same results

    ## End(Not run)

[Package QTLRel version 1.0 Index]