GEVAQuantiles-class: GEVA Quantiles Grouping Results

Description Value Slots Methods

Description

The GEVAQuantiles class represents the results of a quantile detection analysis. For each probe/gene, there is a assigned quantile among the g defined quantiles.

This class inherits from GEVAGroupSet and is inherited by GEVAQuantilesAdjusted.

Value

A GEVAQuantiles object

Slots

grouping

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

scores

numeric vector (m elements) with the assigned quantile scores for each gene/probe
(Inherited from GEVAGroupSet)

ftable

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

centroids

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

offsets

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

info

list of additional information
(Inherited from GEVAGroupSet)

svscores

numeric SVTable (m lines) with individual partial scores for the assigned quantiles

qareasizes

numeric SVTable (g lines) with the S and V sizes for each quantile

qindexes

integer SVTable (g lines) representing the position index to each quantile, in terms of summary and variation

qcount

integer attributes (SVIntAttribute) with the defined number of quantiles for the S and V axes

qcutoff

numeric attributes (SVNumAttribute) with the initial quantile cutoff in S and V, starting from the point zero

qmethod

character, method used to calculate the initial quantiles (see geva.quantiles())

Methods

(See also the inherited methods from GEVAGroupSet)


Conversion and coercion

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

Converts this object to expression

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

Converts this object to SVTable


Plotting

lines(x, ...)

Draws the quantile delimiter lines

plot(x, y, ...)

Draws a SV-plot that highlights the points from each quantile. Dashed lines are included as the quantile delimiters.
Can be combined with another SVTable or GEVAGroupSet given as the y argument to include additional graphical elements


Properties

cluster.method(object)

Returns the option used as the cluster.method argument when calling geva.cluster.
Instances of this object always return 'quantiles'


Sub-slot accessors

classification.table(object) <- value

Sets the data.frame with the qualitative contrasts of classification relevance

classification.table(object)

Gets a data.frame with the qualitative contrasts of classification relevance

quantiles(object)

Gets the unique quantile names


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