runLDmixtureModel: Run LDmixtureModel to a dataset

In yocra3/LDclassifier: Group chromosomes by recombination history

Description

This function makes SNP-blocks and pair them. Then, it applies LDmixtureModel to all SNP-block pairs closer than a selected distance.

Usage

runLDmixtureModel(haplos, annot, blockSize = 2, distance = 1e+05,
  BPPARAM = BiocParallel::SerialParam(1))

Arguments

haplos	Matrix with the haplotypes (SNPs in rows, samples in columns)
annot	GenomicRanges with the SNPs annotation
blockSize	Numeric with the size of the SNP block (Default: 2)
distance	Numeric with the maximum distance in bases to pair two blocks. (Default: 1e5)
BPPARAM	An object from BiocParallelParam. It allow running the models in parallel. By default, the models are run in serial.

Value

A list with the results of the LDmixture models. Each element is a model and contains the following items:

• "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.