LEAPFrOG {LEAPFrOG} | R Documentation |
Provides estimates of admixture proportions and parental divergence of these admixture proportions
LEAPFrOG(data,p,Nudge=0.001,NonLinCon=TRUE)
data |
Vector of allele counts: each element either 0,1,2 or NA. |
p |
Matrix of allele frequencies. Each row corresponds with a SNP. Number of rows must equal length of data. Each column is a population |
Nudge |
D for population 1 will be initialised at 0.5+Nudge. Nudge must be greater than 0. In theory the value for Nudge shouldn't affect the final optimum, but may influence the time to convergence. Default is 0.001. |
NonLinCon |
If TRUE (default), the auglag optimisation function is invoked with a nonlinear constraint imposed on D*m, preventing impossible admixture totals of >1 in the parents. We strongly advise this option |
Standard errors returned in the order P-1 m parameters followed by P-1 D parameters. m and D for the Pth population are not estimated directly and have no standard error.
A list including elements
m |
A vector of admixture proportions in the genotyped offspring, one proportion per population. These sum to 1. |
D |
A vector of parental divergence paramaters, one per population. |
mse |
A vector of length number of populations-. Standard errors for all m estimates save the last populaion |
Dse |
A vector of length number of populations-. Standard errors for all D estimates save the last populaion |
P1 |
Admixture proportions for each population, for parent 'A', derived from the m and D estimates. |
P2 |
Admixture proportions for each population, for parent 'B', derived from the m and D estimates |
value |
Value of the optimised likelihood function. |
counts |
Number of times the likelihood function and gradient function were called during optimisation. |
Daniel Crouch & Michael Weale, Department of Medical and Molecular Genetics, King's College London
#Example with nonsense data – 10000 random SNP genotypes and uniform, random allele frequencies from two populations. library(LEAPFrOG) z1=LEAPFrOG(sample(0:2,10000,replace=TRUE),cbind(runif(10000,0,1),runif(10000,0,1))) z1