R: reconstruct nuclear families

reconstructNPs {GenABEL} | R Documentation

## reconstruct nuclear families

### Description

Function for reconstruction of nulecar families or extended pedigrees based on results of `findRelatives` output (estimatd meiotic distance matrix). Reconstruction is based on the fact that parent-offspring pairs have meiotic distance of '1', and sibs have a distance '2+2'. If both parents and the offspring are genotyped, expected distace between offspring and both parents is '1', and distance between two parents is >2 (coded as 'NA').

### Usage

      reconstructNPs(relationshipGuessMatrix, sex)

### Arguments

`relationshipGuessMatrix` | meiotic relationship matrix, as estimated by `findRelatives`
`sex` | Sex, coded with 1 for males and 0 for females

### Value

A matrix containing reconstructed pedigree(s) coded in linkage-like format. If "fid" is zero, this means that a pedigree could not be assigned.

### Author(s)

Yurii Aulchenko

### Examples

    nloci <- 100
    q <- runif(nloci,min=0.05,max=0.95)
    # g7---g8
    #   _|_
    #  |   |
    # g9  g10---g11
    #       __|_
    #      |   /\
    #    g12 g13 g14
    #
    nids <- 8
    sex <- c(1,0,0,1,0,0,0,0)
    names(sex) <- paste("g",c(7:14),sep="")
    gt <- matrix(ncol=nloci,nrow=nids)
    rownames(gt) <- paste("g",c(7:14),sep="")
    gt["g7",] <- rbinom(nloci,2,q)
    gt["g8",] <- rbinom(nloci,2,q)
    gt["g11",] <- rbinom(nloci,2,q)
    gt["g9",] <- generateOffspring(gt["g7",],gt["g8",],q=q)
    gt["g10",] <- generateOffspring(gt["g7",],gt["g8",],q=q)
    gt["g12",] <- generateOffspring(gt["g10",],gt["g11",],q=q)
    gt["g13",] <- generateOffspring(gt["g10",],gt["g11",],q=q)
    gt["g14",] <- gt["g13",]
    aa<-findRelatives(gt,q=q,nmei=c(1:2))
    aa$guess
    aaPed <- reconstructNPs(aa$guess,sex)
    aaPed

[Package GenABEL version 1.8-0 Index]