runRecombClust: Main function to run all the recombClust pipeline

In isglobal-brge/recombClust: 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

runRecombClust(haplos, annot, clusters = 2, PCs = 3, ...)

Arguments

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
filename	File with genotypic data (SNPs and samples) the data file type must be .vcf (Variant Call Format), .gds (Genomic Data Structure) or .bed (Browser Extensible Data).
start	start position to be treated
end	end position to be treated

Value

A list with four elements:

• class: Cluster classification of the chromosomes

• pc: Responsibilities PCA

• mat: Responsibilities matrix

• models: List of models

isglobal-brge/recombClust documentation built on Nov. 30, 2020, 5:26 p.m.