GEVAGroupedSummary-class: GEVA Grouped Summary-Variation Table

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

Description

The GEVAGroupedSummary class inherits the GEVASummary class and includes group analysis data (e.g., clustering and quantile detection).

Value

A GEVAGroupedSummary object

Slots

sv

numeric matrix composed by two columns: S (summary) and V (variation)
(Inherited from SVTable)

inputdata

GEVAInput-class with the data input
(Inherited from GEVASummary)

sv.method

Names of the statistical methods used to summarize data
(Inherited from GEVASummary)

info

list with additional information
(Inherited from GEVASummary)

groupsetlist

TypedList of GEVAGroupSet objects

Methods

(See also the inherited methods from GEVASummary)

Conversion and coercion

as.expression(x, ginput, ...)

Converts this object to expression

as.matrix(x, ...)

Converts this object to matrix

Plotting

lines(x, ...)

Draws delimiters within quantiles and convex hulls around the clustered points

plot(x, y, ...)

Draws a SV-plot. The horizontal axis is for summary (S) and the vertical axis is for variation (V).
In addition, highlights the included group sets

points(x, ...)

Generic points implementation for GEVAGroupedSummary

Properties

analysis.params(gobject)

Returns a list of analysis parameters passed to geva.cluster to obtain this object

Sub-slot accessors

cluster.method(object)

Gets a character vector listing the cluster.method from each group set

quantiles(object)

Gets the GEVAQuantiles, or NULL if not present

sbcblab/geva documentation built on March 15, 2021, 10:08 p.m.