exprso (version 0.1.8)

ExprsArray-class: An S4 class to store feature and annotation data

Description

An S4 class to store feature and annotation data

Usage

# S4 method for ExprsArray
show(object)
# S4 method for ExprsArray,ANY,ANY,ANY
[(x, i, j)
# S4 method for ExprsArray
$(x, name)
# S4 method for ExprsArray
subset(x, subset, select)
# S4 method for ExprsArray,missing
plot(x, y, a = 1, b = 2, c = 3, ...)
# S4 method for ExprsArray
summary(object)
# S4 method for ExprsArray
getFeatures(object)

Arguments

object, x

An object of class ExprsArray.

i, j

Subsets entire ExprsArray object via object@annot[i, j]. Returns object@annot[, j] if argument i is missing.

name

Returns object@annot[, name].

subset

Subsets entire ExprsArray object via object@annot[subset, ]. Can be used to rearrange feature order.

select

Subsets entire ExprsArray object via object@annot[, select]. Can be used to rearrange subject order.

y

Leave missing. Argument exists because of plot generic definition.

a, b, c

A numeric scalar. Indexes the first, second, and third dimensions to plot. Set c = 0 to plot two dimensions.

...

Additional arguments passed toplot or lattice::cloud.

Methods (by generic)

• show: Method to show ExprsArray object.

• [: Method to subset ExprsArray object.

• $: Method to subset ExprsArray object.

• subset: Method to subset ExprsArray object.

• plot: Method to quickly plot two or three dimensions of data.

• summary: Method to plot summary graphs for a sub-sample of feature data.

• getFeatures: Method to return features within an ExprsArray object.

Slots

exprs

A matrix. Stores the feature data.

annot

A data.frame. Stores the annotation data.

preFilter

Typically a list. Stores feature selection history.

reductionModel

Typically a list. Stores dimension reduction history.

See Also

ExprsArray-class ExprsModel-class ExprsPipeline-class ExprsEnsemble-class ExprsPredict-class