GEVAGroupSet-class: GEVA Grouping Results

Description Value Slots Methods

Description

The GEVAGroupSet class represents the classification of summarized values from a SVTable, where each gene/probe has one assigned group among g defined groups. This is an abstract class. Inherits the GEVACluster and GEVAQuantiles classes.

Value

A GEVAGroupSet object

Slots

grouping

factor (m elements, g levels) used to group the genes/probes

scores

numeric vector (m elements) with the assigned grouping scores for each gene/probe

ftable

data.frame (m lines) with additional grouping features

centroids

numeric SVTable (g lines) with the S and V centroid coordinates for each group

offsets

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

info

list of additional information

Methods


Alternative accessors

levels(x)

Returns the unique group names included in the group set.
Equivalent to levels(groups(x))


Conversion and coercion

as.data.frame(x, row.names = names(x), ...)

Returns a data.frame with the groups and scores slots as columns

as.expression(x, sv, ...)

Gets the expression that reproduces this GEVAGroupSet object, including function parameters used by geva.cluster. The sv argument is optional but can be specified to replace the source SVTable

as.SVTable(x, which = c("sv", "offsets", "centroids"), ...)

Retrieves a SVTable based on the contents indicated by which. The accepted arguments are: sv for the source data; offsets for the offsets slots; and centroids for the centroids slot


Dimension accessors

length(x)

Returns the number of rows in the sv slot

names(x)

Gets the assigned names by the classification and scores


Plotting

color.values(x, point.col = NULL, ...)

Gets the colors associated to the grouped data points. If not present, generates random group colors.
If point.col is a single character or an vector of the same length of data points, adjusts the color values to web RGBA

plot(x, y, ...)

Draws a SV-plot that highlights the grouped information.
Can be combined with another SVTable or GEVAGroupSet given as the y argument to include additional graphical elements

points(x, ...)

Draws the grouped points


Properties

analysis.params(gobject)

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

cluster.method(object)

Returns the option used as the cluster.method argument when calling geva.cluster


Sub-slot accessors

classification.table(object) <- value

Stores the classification data.frame on this object

classification.table(object)

Returns a data.frame of predicted classifications, if supported by this object

sv.data(object)

Returns a SVTable with the source SV coordinates

sv(object)

Returns the numeric matrix in the SVTable from sv.data(object)


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