CalculateMom {Jacquard} | R Documentation |
Function CalculateMom
computes moment estimators for a set of
relatedness parameters (kinship, inbreeding, least one IBD out of three
and T4) using the genotype data and the allele frequencies.
CalculateMom(Xgen, mafvec, ind.sub = 1:nrow(Xgen), verbose = TRUE)
Xgen |
Genotype data coded in (0,1,2) format |
mafvec |
A vector of minor allele frequencies |
ind.sub |
Index for subsetting individuals |
verbose |
Print output on the progress of the algorithm if |
A list object with four fields:
T1 |
The pairwise coancestry or kinship coefficients (symmetric) |
T2 |
The pairwise inbreeding coefficients (non-symmetric) |
T3 |
The pairwise Least one IBD out of three (symmetric) |
T4 |
T4 (skew-symmetric) |
Jan Graffelman (jan.graffelman@upc.edu)
Csuros, M. (2014) Non-identifiability of identity coefficients at biallelic loci. Theoretical Population Biology 92, pp. 22-29. doi:10.1016/j.tpb.2013.11.001.
data(SimulatedPedigree)
Xgen <- as.matrix(SimulatedPedigree[,6:ncol(SimulatedPedigree)])
mafvec <- mafvector(Xgen)
Theta.mom <- CalculateMom(Xgen[1:10,],mafvec)