GEVAInput-class: GEVA Input Data
In sbcblab/geva: Gene Expression Variation Analysis (GEVA)

Description Value Slots Methods

The GEVAInput class contains the initial data for GEVA usage. It stores numeric matrices of logFC values from differential expression comparison results. Options for calculations and summarizing are also included.

A GEVAInput object

values: numeric matrix (m*n) of log-ratio values, usually logFC
weights: numeric matrix (m*n) of weighted values. If not defined, all weight values are equal to 1
factors: factor (n elements) representing the grouping of the n columns. If not defined, all factors are equal to NA
ftable: data.frame with m rows containing attribute columns associated to the features (e.g., probes or genes)
info: list of supplementary information related to the input

Alternative accessors

levels(x): Returns the unique values from the assigned factors; or NA if there are no assigned factors in x

Conversion and coercion

as.array(x, ...): Converts this object to array

Dimension accessors

dim(x): Gets the dimensions defined for both matrices in values and weights slots
dimnames(x) <- value: Sets the list with the row and column names.
Individual dimension names can also be set using rownames<- and colnames<-
dimnames(x): Gets a list with the row and column names.
Individual dimension names can also be accessed through rownames and colnames
inputnames(object): Gets the input column names (same as colnames(object))
length(x): Returns the number of rows in the values slot
names(x): Same as inputnames. For internal use

Plotting

plot(x, y, ...): Summarizes the input using the default parameters, then calls the plot on the returned GEVASummary object.
Not intended to regular use and will give a warning if called

Properties