GENLIB (version 1.0.3)

gen.simuSet: Gene dropping simulations with specified transmission probabilities

Description

Returns the number of alleles transmitted to specified probands from ancestors considering sepcified transmission probabilities.

Usage

gen.simuSet(gen, pro, ancestors, stateAncestors, 
                   probMatrix=matrix(c(
                                    c(1,0.5,0,0.5,0.25,0,0,0,0,1,1,1,1,0.75,0.5,1,0.5,0),
                                    c(1,0.5,0,0.5,0.25,0,0,0,0,1,1,1,1,0.75,0.5,1,0.5,0)),
                                     nrow=3, ncol=12),
                   simulNo = 5000)

Value

A matrix with number of columns equal to the number of simulations and number of rows equal to the number of probands.

See Also

gen.genealogy gen.simuProb gen.simuSample

Examples

A case where only male subjects can receive alleles
data(geneaJi) 
genJi<-gen.genealogy(geneaJi) 
onlyThroughMale<-matrix(c(c(1,0.5,0,0.5,0.25,0,0,0,0,1,1,1,1,0.75,0.5,1,0.5,0), rep(1,18)), 
                        nrow=3, ncol=12) 
gen.graph(genJi, indVarAffected=c(28,27,25,17,12,8,4,1), varAffected=c(28,27,25,17,12,8,4,1))
simu_1000a<-gen.simuSet(genJi, pro=c(1,28), ancestors=c(17,25), stateAncestors=c(1,1), 
                        simulNo = 1000,probMatrix=onlyThroughMale)
Number of alleles received by probants
table(simu_1000a)
Number of alleles received by all probants at each simulation
table(colSums(simu_1000a))
Number of alleles received by each probant
table(simu_1000a[1,],simu_1000a[2,])

A case where subjects are limited to one copy compared to what is normally expected
max1Allreceived<-matrix(rep(c(1,0.5,0,0.5,0.25,0,0,0,0,1,1,1,1,1,1,1,1,1), 2) , nrow=3, ncol=12)  
gen.graph(genJi)
simu_1000b<-gen.simuSet(genJi, pro=c(1,29), ancestors=25, stateAncestors=1, simulNo=10000,
                        probMatrix=max1Allreceived)
Normal case matrix not changed
simu_1000original<-gen.simuSet(genJi, pro=c(1,29), ancestors=25, stateAncestors=1, simulNo=10000)
Number of alleles received by each probant
table(simu_1000b) 
table(simu_1000original) 
Number of alleles received by all probants at each simulation
table(colSums(simu_1000b)) 
table(colSums(simu_1000original)) 
Number of alleles received by each probant
table(simu_1000b[1,],simu_1000b[2,])
table(simu_1000original[1,],simu_1000original[2,])