| 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
# 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