GEVAResults-class: GEVA Results Table

Description Value Slots Methods

Description

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).

Value

A GEVAResults object

Slots

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

Methods


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


nunesijg/geva documentation built on March 12, 2021, 3:58 p.m.