marker.cluster: marker.cluster

In mtmcgowan/GGcall: Clusters Infinium SNP chip data in polyploid species and calls genotypes

Description

Clusters a single markers with Rmixmod

Usage

marker.cluster(marker, data.type = "raw", iteration = 5,
  model.list = c("Gaussian_pk_Lk_Ck", "Gaussian_pk_Lk_Bk"), clust.num = 8)

Arguments

marker	A project object, must be formatted correctly according to the project.create function
data.type	A string variable indicating which data should be used for clustering. ('raw', 'GSnorm','GStrans', 'thetaonly')
iteration	The number of times to re-cluster (can result in more stable results, but slows clustering time)
model.list	A list of Rmixmod models to use for cluster (Refer to Rmixmod documentation for more info)
clust.num	The maximum number of clusters to test for (lowering this speeds clustering time)

Details

USes the 'Rmixmod' package to fit a Gaussian mixture model using a supplied model list

Value

A marker object updated with the best clustering result out of a defined number of iterations

This function relies on the following packages: Rmixmod

mtmcgowan/GGcall documentation built on July 1, 2021, 4:14 a.m.