woparent.BestRepeat {BestRepeat} | R Documentation |
The program calculates the optimal number of repeated measurements for variance components models for nuclear families when parental phenotypes are not available.
woparent.BestRepeat(Vm, cost.pheno, Va, Vg, Ve, s)
Vm |
Measurement error variance |
cost.pheno |
Ratio of phenotyping cost to genotyping and subject recruitment cost |
Va |
Major gene effect, the additive genetic variance due to the major gene |
Vg |
Polygenic variance which is the genetic variance due to all residual additive effects not explained by the QTL |
Ve |
Subject-specific environmental variance |
s |
Number of offspring per family |
The model assums the total trait variance = Va + Vg + Ve + Vm
The function returns the optimal number of repeated measures.
Wei-Min Chen and Liming Liang
Liang L, Chen WM, Sham PC and Abecasis GR. Variance Components Linkage Analysis with Repeated Measurements (2008)
BestRepeat
, BestRepeat-package
#Suppose that the genotyping plus recruitment cost per subject is 5 times the phenotyping cost per measure. #The measurement error variance is 40. #Major gene effect is 20, the polygene effect is 40 and the environmental variance is 40. #There are 4 offspring per nuclear family where parental phenotypes are not available. #The optimal number of repeated measures is given by woparent.BestRepeat(Vm=40,cost.pheno=0.2,Va=20,Vg=40,Ve=40,s=4)