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

Description Value Slots Methods

The GEVAQuantilesAdjusted class represents the results of a quantile detection analysis with adjusted assignments based on relationships with other GEVAGroupSet objects. For each probe/gene, there is a assigned quantile among the g defined quantiles.

This class inherits from GEVAQuantiles.

A GEVAQuantilesAdjusted 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 data
(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
(Inherited from GEVAQuantiles)
qareasizes: numeric SVTable (g lines) with the S and V sizes for each quantile
(Inherited from GEVAQuantiles)
qindexes: integer SVTable (g lines) representing the position index to each quantile, in terms of summary and variation
(Inherited from GEVAQuantiles)
qcount: integer attributes (SVIntAttribute) with the defined number of quantiles for the S and V axes
(Inherited from GEVAQuantiles)
qcutoff: numeric attributes (SVNumAttribute) with the initial quantile cutoff in S and V, starting from the point zero
(Inherited from GEVAQuantiles)
grouprels: TypedList of named factor elements representing external group relationships to the current quantiles