inversionModel: Run LDmixture model to a pair of SNP-blocks

In yocra3/LDclassifier: Group chromosomes by recombination history

Description

Run LDmixture model to a pair of SNP-blocks

Usage

inversionModel(dat, maxSteps = 1000, prob0 = 0.5)

Arguments

dat	Matrix with the genotype data
maxSteps	Numerical with the maximum number of iterations run by the EM algorithm
prob0	Initial mixture probability.

Value

A list with the LDmixture results

• "logMix"Log-likelihood of mixture model

• "logLD"Log-likelihood of linkage model

• "logNoLD"Log-likelihood of recomb model

• "BIC"BIC of the mixture vs the base model

• "prob"Proportion of chromosomes belonging to recomb model

• "steps"Number of iterations until converge of the EM algorithm

• "pval"P-value of the Chi-square test

• "r1"Responsibilities for recomb population of each chromosomes. It is only available for selected models (BIC > 10, pval > 0.05)

yocra3/LDclassifier documentation built on May 27, 2019, 12:13 p.m.