get cluster membership matrix

cmeans_matrix {geneExpression}

R Documentation

get cluster membership matrix

Description

Usage

cmeans_matrix(pattern,
    memberCutoff = 0.8,
    empty.shared = 2,
    max.cluster.shared = 3);

Arguments

pattern

the cmeans clustering result, which can be an ExpressionPattern object, a data frame object of the membership matrix, or a pipeline object that produces a set of the EntityClusterModel cluster model data.

memberCutoff

the membership cutoff value for assign a gene feature into the target cluster: the gene feature will be assigned into the cluster if its membership value is greater than this threshold ratio of the max membership value of the corresponding cluster. [as double]

empty.shared

how many clusters will be assigned to a gene feature when there is no cluster that its membership value is greater than the memberCutoff threshold. [as integer]

max.cluster.shared

the max cluster numbers that a gene feature can be assigned into. [as integer]

env

the R# runtime environment object. [as Environment]

Authors

phenotype_kit

Value

a vector of the EntityClusterModel cluster model data: the ID property is the gene feature id, the Properties property is the membership value of the gene feature to each cluster(#1, #2, ...), and the Cluster property is the cluster tag that the gene feature has been assigned into(multiple cluster tags are joined by the ; character);

this function returns a R# error message object if the input data can not be cast to a collection of the cluster model data.

clr value class

EntityClusterModel

[Package geneExpression version 1.0.0.0 Index]