GEVAResults-class: GEVA Results Table
In sbcblab/geva: Gene Expression Variation Analysis (GEVA)

Description Value Slots Methods

The GEVAResults class contains the final results from GEVA analyses. It represents the results of multiple statistical approaches from summary/variation data, clustering, quantile detection, and factor analysis (if applicable).

A GEVAResults object

resultstable: data.frame (m lines) with classification results for the genes/probes
svdata: GEVASummary used as input
quantdata: GEVAQuantiles or GEVAQuantilesAdjusted with the final quantile assignments for the summarized data
factoring: data.frame (m lines) with detailed results for the factor analyses, such as p-values for each factor. If there was no factor analysis, this slot is NULL or empty
classiftable: data.frame used as reference for the final classification
info: list of supplementary information

Conversion and coercion

as.expression(x, gsummary, gquants, ...): Gets the expression that reproduces this GEVAResults object, including function parameters used by geva.finalize. The gsummary and gquants arguments are optional but can be specified to replace the internal GEVASummary and GEVAQuantiles, respectively

Dimension accessors

dim(x): Returns the dimensions from the resultstable slot
dimnames(x): Returns a list with the row and column names from the results.table slot.
Individual dimension names can also be accessed through rownames and colnames
length(x): Returns the number of rows in the resultstable slot
names(x): Returns the column names from the resultstable slot

Plotting

plot(x, y, ...): Draws a SV-plot that highlights the relevant points from adjusted quantiles
points(x, which, ..., classif): Draws the results points.
If which (character vector) is given, plots only the matching genes/probes.
If classif (character vector) is given, plots only points with the matching classification

Properties

x$name <- value: Extracts a column from the resultstable slot
x[i, j, ..., drop=TRUE]: Extracts the contents from the resultstable slot
analysis.params(gobject): Returns a list of analysis parameters passed to geva.finalize or geva.quick to obtain this object

Sub-slot accessors

featureTable(object): Returns the features data.frame from the internal GEVAInput
head(x, ...): Returns the first lines of results.table(x)
inputdata(object): Returns the internal GEVAInput
inputvalues(object): Returns the values matrix from the internal GEVAInput
inputweights(object, normalized): Returns the weights matrix from the internal GEVAInput
levels(x): Returns the factors used in factor analysis, if present