GEVAGroupSet-class: GEVA Grouping Results
In nunesijg/geva: Gene Expression Variation Analysis (GEVA)

Description Value Slots Methods

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.

A GEVAGroupSet object

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

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)