genecl-class {cogena} | R Documentation

## An S4 class to represent co-expressed gene

### 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

[Package cogena version 1.14.0 Index]