geno_logL_ssq function

Calculate a matrix of sum-of-squares of genotype log-likelihoods for a genetic dataset

Takes a list of key parameters from a genetic dataset, and calculates the sum of squared log-likelihood of each individual's genotype, given the allele counts in each collection. This is used for the quick-and-dirty Z-score calculations.

geno_logL_ssq(par_list)

Arguments

• par_list: genetic data converted to the param_list format by tcf2param_list

Returns

geno_logL returns a matrix with C rows and I columns. Each column represents an individual, and each row the log-likelihood of that individual's genotype, given the allele counts in that collection

Details

Leave-One-Out cross-validation is used to avoid bias in log-likelihood for an individual's known collection of origin

Examples

example(tcf2param_list)
ale_glL <- geno_logL(ale_par_list)