CellMix 1.6

Factory Method for ExpressionMix Objects

Description

This is a generic function that creates instances of ExpressionMix-class objects from common input data.

Usage

ExpressionMix(object, ...)

S4 (ExpressionMix)
`show`(object)

S4 (ExpressionSet)
`ExpressionMix`(object, ..., composition = nmfModel(object))

S4 (matrix)
`ExpressionMix`(object, ..., composition = nmfModel(object))

S4 (character)
`ExpressionMix`(object, no.pure = FALSE, verbose = FALSE, ...)

Arguments

object
main input data. See possible values in section Methods.
...
extra arguments to allow extension. See each method's description for more details.
composition
an NMF-class object, that contains the mixture data (signatures and/or proportions).
no.pure
a logical that indicates if the pure samples should be filtered out.
verbose
logical that indicates if log messages should be shown.

Value

an ExpressionMix-class object

Methods

  1. ExpressionMixsignature(object = "ExpressionSet"): Creates an ExpressionMix object from an ExpressionSet object.

  2. ExpressionMixsignature(object = "matrix"): Creates an ExpressionMix object using the matrix object as the expression matrix.

  3. ExpressionMixsignature(object = "character"): Creates an ExpressionMix object from the accession key of a registered dataset.

    The expression data is first loaded with gedData -- as an ExpressionSet object. The mixture data is then built as an NMF-class object and put together with the expression data into a new ExpressionMix-class object.