Geneset.intersectSelection

The output of the <code>PathwaysIter</code> function.

list.output

The significance level to be handled for cutting of the
pathways. Default is 0.05.

sign

Optional. Names of the methods. Default is NULL.

names

Logical. If TRUE, a separate element is created per
cluster containing the pathways for each iteration. Default is FALSE.

seperatetables

Logical. If TRUE, the p-values of the each iteration of
each pathway in the intersection is given. If FALSE, only the mean p-value
is provided. Default is FALSE.

separatepvals

Internal function of <code>Geneset.intersect</code>.

Several integrative data methods in which information of objects from different data sources can be combined are included in the IntClust package. As a single data source is limited in its point of view, this provides more insight and the opportunity to investigate how the variables are interconnected. Clustering techniques are to be applied to the combined information. For now, only agglomerative hierarchical clustering is implemented. Further, differential gene expression and pathway analysis can be conducted on the clusters. Plotting functions are available to visualize and compare results of the different methods.

Geneset.intersectSelection: Intersection over resulting gene sets of `PathwaysIter` function for a selection of objects

Description

Usage

Arguments