reconstructNPs: reconstruct nuclear families

Description Usage Arguments Value Author(s) Examples

View source: R/reconstructNPs.R

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

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  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

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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.

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