Segregate di-allelic genes down through the generations of a pedigree. It is assumed that the founders are independent and that the genes are in Hardy Weinberg equilibrium in the population.
segregate.genes(pedigree, maf)
| pedigree | a |
|---|---|
| maf | a vector of minor allele frequencies for each diallelic gene to segregate through the pedigree |
Returns a data frame. Each row matches the order of the individuals in the pedigree and each column corresponds to each of the segregated genes. The data frame contains values 0, 1, or 2 corresponding to the number of copies of the minor allele frequency allele that person has.
pedigree, kinship,
library(kinship2) mydata <- data.frame(id=1:5, dadid=c(NA, NA, 1, 1, 1), momid=c(NA, NA, 2, 2, 2), sex=c("male", "female", "male", "male", "male"), famid=c(1,1,1,1,1)) relation <- data.frame(id1=c(3), id2=c(4), famid=c(1), code=c(1)) ped <- pedigree(id=mydata$id, dadid=mydata$dadid, momid=mydata$momid, sex=mydata$sex, relation=relation) segregate.genes(ped, c(.1, .3, .5))#> gene1 gene2 gene3 #> [1,] 1 1 2 #> [2,] 0 0 0 #> [3,] 0 1 1 #> [4,] 0 1 1 #> [5,] 1 1 1