genecl_class: An S4 class to represent co-expressed gene

In cogena: co-expressed gene-set enrichment analysis

Description

An S4 class to represent co-expressed gene

Slots

mat

Differentially expressed gene expression profilings. Either a numeric matrix, a data.frame, or an ExpressionSet object. Data frames must contain all numeric columns. In all cases, the rows are the items to be clustered (e.g., genes), and the columns are the samples.

clusterObjs

a list contains clustering results.

Distmat

the distance matrix.

clMethods

clustering method.

labels

the label of genes

nClust

A numeric vector giving the numbers of clusters to be evaluated. e.g., 2:6 would evaluate the number of clusters ranging from 2 to 6.

metric

the distance measure to be used. It must be one of "euclidean","maximum", "manhattan", "canberra", "binary", "pearson", "abspearson", "correlation", "abscorrelation", "spearman" or "kendall". Any unambiguous substring can be given. In detail, please reference the parameter method in amap::Dist. Some of the cluster methods could use only part of the metric. Please reference the manual of cogena.

method

For hierarchical clustering (hclust and agnes), the agglomeration method used. The default is "complete". Available choices are "ward", "single", "complete", and "average".

ncore

the number of cores used.

call

the called function

cogena documentation built on Nov. 8, 2020, 6:54 p.m.