GEVAQuantiles-class: GEVA Quantiles Grouping Results
In sbcblab/geva: Gene Expression Variation Analysis (GEVA)

Description Value Slots Methods

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.

A GEVAQuantiles object

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())

(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