R: Genetic contribution of ancestors

gen.gc {GENLIB} | R Documentation

## Genetic contribution of ancestors

### Description

Returns the genetic contribution of ancestors to the gene pool of sepcifiec probands

### Usage

    gen.gc(gen, pro=0, ancestors=0, vctProb=c(0.5,0.5,0.5,0.5), typeCG="IND")

### Arguments

`gen` | An object of class GLgen obtained with gen.genealogy, gen.lineages or gen.branching. Required.
`pro` | Vector of proband id numbers to be included. Default is 0, which will select all individuals without children.
`ancestors` | Vector of ancestors id numbers to be included. Default is 0, which will select all individuals without parents.
`vctProb` | Vector of transmission probabilities. The first two values indicate the probabilities of transmission of a father to his son and daughter, respectively, and the following two values are the same for the mother. Default is vctProb=c(0.5,0.5,0.5,0.5).
`typeCG` | IF typeCG="IND" (default), the genetic contribution from each ancestor is calculated for each proband. If typeCG="MEAN", the average (over all probands) genetic contributions of each ancestor is returned. If typeCG="PRODUCT", the product (over all probands) of genetic contributions is returned for each ancestor. If typeCG="TOTAL", the sum (over all probands) of genetic contributions is returned for each ancestor. If typeCG="CUMUL", ancestors are ranked in decreasing order of total contribution and cumulative contribution is returned.

### Value

A matrix with rows corresponding to probands and columns corrsponding to ancestors when typeCG="IND". For the other typeCG values, rows are ancestors and there is one column containing mean, product, total or cumulative values.

### References

Roberts DF. (1968) Genetic effects of population size reduction. Nature, 220, 1084-1088.

O'Brien E, Jorde LB, Ronnlof B, Fellman JO, Eriksson AW. (1988) Founder effect and genetic disease in Sottunga, Finland. American Journal of Physical Anthropology, 77, 335-346.

### See Also

`gen.genealogy` `gen.rec` `gen.occ` `gen.implex` `gen.meangendepth` `gen.completeness`

### Examples

    data(geneaJi)
    genJi<-gen.genealogy(geneaJi)
    gc<-gen.gc(genJi, pro=c(1,29), ancestors=c(3,6,10,12,14,16,18,20,26,28))
    gc
    gc_cum<-gen.gc(genJi, pro=c(1,29), ancestors=c(3,6,10,12,14,16,18,20,26,28), type="CUMUL")
    gc_cum

    data(genea140)
    gen140<-gen.genealogy(genea140)
    gc<-gen.gc(gen140, pro=c(454422,676521,677273,717537,717634,717709,868572),
               ancestors=c(18305,18528,31114,18325))
    gc
    ## Not run: Mother-daughter transmission only with probability=0.5
    gc_MoLi<-gen.gc(gen140, pro=c(217891,302718,409282,802424,409682,443151),
    		ancestors=c(18321,218231,296200,39066,18679,442607),vctProb=c(0,0,0,0.5))
    gc_MoLi

[Package GENLIB version 1.0.6 Index]