GENLIB (version 1.0.4)

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)

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. Required.

ancestors

Vector of ancestors id numbers to be included. Required.

stateAncestors

Required vector indicating, for each ancestor in ancestors, the genotype state:

0 = no disease allele present

1 = 1 disease allele present

2 = 2 disease alleles present

probMatrix

Matrix of transmission probabilities of 0, 1, or 2 disease alleles. Default is:

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]

[1,] 1.0 0.50 0 1 1.00 1.0 1.0 0.50 0 1 1.00 1.0

[2,] 0.5 0.25 0 1 0.75 0.5 0.5 0.25 0 1 0.75 0.5

[3,] 0.0 0.00 0 1 0.50 0.0 0.0 0.00 0 1 0.50 0.0

where rows are genotype states (0,1,2) for the father and columns are states for the mother (in blocks of 3).

1st block (col 1-3) are the probabilities of transmitting 0 allele to a son.

2nd block (col 4-6) are the probabilities of transmitting 1 allele to a son.

3rd block (col 7-9) are the probabilities of transmitting 0 allele to a daughter.

4th block (col 10-12) are the probabilities of transmitting 1 allele to a daughter.

simulNo

Number of simulations to perform. Default is 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

# NOT RUN {
A case where only male subjects can receive alleles
# }
# NOT RUN {
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)
# }
# NOT RUN {
Number of alleles received by probants
# }
# NOT RUN {
table(simu_1000a)
# }
# NOT RUN {
Number of alleles received by all probants at each simulation
# }
# NOT RUN {
table(colSums(simu_1000a))
# }
# NOT RUN {
Number of alleles received by each probant
# }
# NOT RUN {
table(simu_1000a[1,],simu_1000a[2,])

# }
# NOT RUN {
A case where subjects are limited to one copy compared to what is normally expected
# }
# NOT RUN {
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)
# }
# NOT RUN {
Normal case matrix not changed
# }
# NOT RUN {
simu_1000original<-gen.simuSet(genJi, pro=c(1,29), ancestors=25, stateAncestors=1, simulNo=10000)
# }
# NOT RUN {
Number of alleles received by each probant
# }
# NOT RUN {
table(simu_1000b) 
table(simu_1000original) 
# }
# NOT RUN {
Number of alleles received by all probants at each simulation
# }
# NOT RUN {
table(colSums(simu_1000b)) 
table(colSums(simu_1000original)) 
# }
# NOT RUN {
Number of alleles received by each probant
# }
# NOT RUN {
table(simu_1000b[1,],simu_1000b[2,])
table(simu_1000original[1,],simu_1000original[2,]) 
# }