project.cluster: project.cluster

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

Description

Cluster markers in Parallel with Rmixmod

Usage

project.cluster(project, marker.indices = NULL, data.type = "raw.scaled",
  iteration = 5, model.list = c("Gaussian_pk_L_Ck", "Gaussian_pk_L_Bk"),
  clust.num = 8)

Arguments

project	A project object, must be formatted correctly according to the project.create function
marker.indices	The indices of the markers to cluster
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 increases 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

Sets up a parallel backend and clusters each marker using mixture of gaussian models provided by the 'Rmixmod' package.

Value

A project object updated with clustering models

This function relies on the following packages:

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