reconstructNPs: reconstruct nuclear families

In GenABEL: genome-wide SNP association analysis

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

GenABEL documentation built on May 30, 2017, 3:36 a.m.