segregate.genes: Segregate genes through a pedigree

In ekstroem/MESS: Miscellaneous Esoteric Statistical Scripts

Segregate genes through a pedigree

Description

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.

Usage

segregate.genes(pedigree, maf)

Arguments

pedigree	a pedigree object
maf	a vector of minor allele frequencies for each diallelic gene to segregate through the pedigree

Value

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.

Author(s)

Claus Ekstrom [e-mail]

See Also

pedigree, kinship,

Examples

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))

ekstroem/MESS documentation built on July 28, 2023, 4:02 a.m.