R: Gene dropping simulations with specified transmission...

gen.simuSet {GENLIB} | R Documentation

## 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
    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
    table(simu_1000a)
    ## Not run: Number of alleles received by all probants at each simulation
    table(colSums(simu_1000a))
    ## Not run: Number of alleles received by each probant
    table(simu_1000a[1,],simu_1000a[2,])

    ## Not run: 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)
    ## Not run: Normal case matrix not changed
    simu_1000original<-gen.simuSet(genJi, pro=c(1,29), ancestors=25, stateAncestors=1, simulNo=10000)
    ## Not run: Number of alleles received by each probant
    table(simu_1000b)
    table(simu_1000original)
    ## Not run: Number of alleles received by all probants at each simulation
    table(colSums(simu_1000b))
    table(colSums(simu_1000original))
    ## Not run: Number of alleles received by each probant
    table(simu_1000b[1,],simu_1000b[2,])
    table(simu_1000original[1,],simu_1000original[2,])

[Package GENLIB version 1.0.6 Index]