fam2r-package: From 'Familias' to R

In fam2r: From 'Familias' to R

Description

Conditional simulation of marker data on pedigrees, plotting and likelihood calculations, using Familias or paramlink, on pedigrees. The package is specifically tailored to work on export of data from windows Familias.

Details

The main function is conditionalLR. Marker data for a specified individual is simulated conditionally on pedigrees and previously typed individuals using markerSim. Then likelihoods are calculated using Familias or paramlink.

Author(s)

Thore Egeland <[e-mail]> and Magnus Dehli Vigeland.

Maintainer: Thore Egeland

References

Kling et al (2017)

Examples

# Example.There is one marker. A grand mother (GM=1) is
# is genotyped and we simulate the genotype of the grand son (GS=POI).
data(grandmother)
pedigrees = grandmother$pedigrees
datamatrix = grandmother$datamatrix
loci = grandmother$loci
x = Familias2linkdat(pedigrees, datamatrix, loci)
missing.person.plot(x[[1]], missing=3, marker = 1, newdev=TRUE)
Nsim = 5 #Increase to 1000
# Calculations can be done using 'Familias' or 'paramlink':
res1 = FamiliasConditional(Nsim = Nsim, datamatrix, loci, pedigrees, 
  truePed = 1, available = "GS", ref=2, seed=17)
res2 = paramlinkConditional(Nsim = Nsim, datamatrix,  loci, pedigrees, 
  truePed = 1, available = "GS", ref=2, seed=17)
LR1 = data.frame(LR.H1.Familias=res1[[1]][,1], LR.H1.paramlink=res2[[1]][,1])
# Checks that 'Familias' and 'paramlink' gives the same result:
stopifnot(all(apply(LR1,1, function(x) abs(x[1]-x[2])<1e-10)))

# Altenatively, there is a wrapper function
res3 = conditionalLR(Nsim = Nsim, datamatrix, loci, pedigrees, 
  available = "GS", ref=2, seed=17, verbose=FALSE, 
  program="Familias", simplify=TRUE)
	 

fam2r documentation built on May 2, 2019, 1:09 p.m.