eSet-class {Biobase}R Documentation

Class "eSet": a new exprSet class

Description

A second attempt at a universal definition of experimental data, combined with phenotypic data and in some cases probe data.

Objects from the Class

Objects can be created by calls of the form new("eSet", ...). These objects are basically structured to provide a unified and simplified set of methods for handling experimental data. This might be gene expression data, array CGH data or SELD-TOF/MALDI-TOF data.

Slots

eList:
Object of class "exprList" containing the experimental data.
phenoData:
Object of class "phenoData" containing the phenotypic or sample level data.

Methods

[
signature(x = "eSet"): basic subsetting. It returns an object of class eSet. The first index subsets experimental units while the second subsets samples.
combine
signature(x = "eSet", y = "eSet"): a method for merging two eSets. Substantial checking is carried out.
combine
signature(x = "eSet", y = "ANY"): As above.
eList
signature(object = "eSet"): a container for the experimental data. This can accomodate multiple channels etc.
eList<-
signature(object = "eSet", value = "exprList"): An assignment function for exprLists.
eList<-
signature(object = "eSet", value = "environment"): as above
eList<-
signature(object = "eSet", value = "list"): as above.
exprs
signature(object = "eSet"): extract the experimental data.
getExpData
signature(object = "eSet", name = "character"): extract the experimental data.
pData
signature(object = "eSet"): get the actual data.frame containing the phenotypic data.
pData<-
signature(object = "eSet"): replace the actual data.frame containing the phenotypic data.
phenoData
signature(object = "eSet"): extract the phenoData object (data frame plus descriptions of the covariates).
phenoData<-
signature(object = "eSet", value = "phenoData"): a replacement method for the phenoData object.
show
signature(object = "eSet"): a print method, to control printing vast amounts of data.

Note

The data structures etc. were designed by a consensus view of Biocore.

Author(s)

Biocore

See Also

exprSet-class

Examples

##---- Should be DIRECTLY executable !! ----

[Package Biobase version 1.4.15 Index]