runLDclassifier: Main function to run all the LDclassifier pipeline

In yocra3/LDclassifier: Group chromosomes by recombination history

Description

This function takes as input phased chromosomes and returns the responsibilities PCA and the cluster classification of the samples.

Usage

runLDclassifier(haplos, annot, clusters = 2, PCs = 1, ...)

Arguments

haplos	Matrix with the haplotypes (SNPs in rows, samples in columns)
annot	GenomicRanges with the SNPs annotation
clusters	Numeric with the clusters used in k-means
PCs	Numeric with the number of PCA components used to make the clustering.
...	Further arguments passed to runLDmixtureModel

Value

A list with two elements:

• "class"Cluster classification of the chromosomes

• "pc"Responsibilities PCA

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