top_genes_cluster_tissues {EMMIXgene}

Cluster tissues

Description

Cluster tissues

Usage

top_genes_cluster_tissues(gen, n_top = 100, method = "mfa", q = 2, g = 2)

Arguments

gen

An EMMIXgene object produced by select_genes().

n_top

number of top genes (as ranked by likelihood) to be selected

method

Method for separating tissue classes. Can be either 't' for a univariate mixture of t-distributions on gene cluster means, or 'mfa' for a mixture of factor analysers.

q

number of factors if using mfa

g

number of components if using mfa

Value

An EMMIXgene object containing:

stat

A matrix containing clustering (0 or 1) for each sample (columns) by each group(rows).

top_gene

The row numbers of the top genes.

fit

The fit object used to determine the clustering.

Examples

alon_sel <- select_genes(alon_data[seq_len(100), ])
alon_top_10<-top_genes_cluster_tissues(alon_sel, 10, method='mfa', q=3, g=2)