cogena_class: An S4 class to represent co-expressed gene-set enrichment...

In zhilongjia/cogena: co-expressed gene-set enrichment analysis

An S4 class to represent co-expressed gene-set enrichment analysis result.

Description

An S4 class to represent co-expressed gene-set enrichment analysis result.

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.

measures

a list of the enrichment results.

upDn

the enrichment score for up or down-regulated genes.

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".

annotation

logical matrix of biological annotation with row be DE gene column be gene sets and value be logical.

sampleLabel

character vector with names are sample names. Only used for plotting.

ncore

the number of cores used.

gmt

the gmt file used

call

the called function

zhilongjia/cogena documentation built on Nov. 21, 2023, 1:34 a.m.