GEVACluster-class: GEVA Clustering Results

In nunesijg/geva: Gene Expression Variation Analysis (GEVA)

Description

The GEVACluster class represents the classification results from a cluster analysis. For each probe/gene, there is a assigned cluster among the g defined clusters.

This class inherits from GEVAGroupSet.

Value

A GEVACluster object

Slots

grouping

factor (m elements, g levels), cluster assignment for each gene/probe
(Inherited from GEVAGroupSet)

scores

numeric vector (m elements) comprising a score value for each cluster assignment
(Inherited from GEVAGroupSet)

ftable

data.frame (m lines) with additional cluster assignment features
(Inherited from GEVAGroupSet)

centroids

numeric SVTable (g lines) with the S and V centroid coordinates for each cluster
(Inherited from GEVAGroupSet)

offsets

numeric SVTable (m lines) with the S and V coordinate offsets each gene/probe from its cluster centroid
(Inherited from GEVAGroupSet)

info

list of supplementary information
(Inherited from GEVAGroupSet)

cluster.method

character, method used in the cluster analysis (see geva.cluster)

Methods

(See also the inherited methods from GEVAGroupSet)

Plotting

lines(x, ...)

Draws convex hulls around the clustered points

plot(x, y, ...)

Draws a SV-plot that highlights the clustered points. Convex hulls are included for visual purposes only and do not avoid enclosing points from other clusters on concave parts.
Can be combined with another SVTable or GEVAGroupSet given as the y argument to include additional graphical elements

nunesijg/geva documentation built on March 12, 2021, 3:58 p.m.