make.dex.set.object {AGDEX} | R Documentation |
This function generates a list object containing four components for function agdex()
make.dex.set.object(Eset.data, comp.var, comp.def, gset.collection)
Eset.data |
an ExpressionSet object carries the gene expression data (Exprs) and Phenotype data (pData) |
comp.var |
the column name or numeric index for group labels in pData of object Eset.data |
comp.def |
a string definition of comparison, group labels connected by "-" |
gset.collection |
an object belongs to class GeneSetCollection |
The ExpressionSet includes two components: exprs: a matrix of expression values pData: a data frame contains the sample IDs and their assigned group labels.
gset.collection contains a GeneSetCollection object defined in the Bioconductor package GSEABase. The gset.collection object must use the same identifiers for probe-sets as that used in the exprs component of Eset.data.
A list object containing the four components described in argument section.
Stan Pounds <stanley.pounds@stjude.org; Cuilan Lani Gao <cuilan.gao@stjude.org>
ExpressionSet class: ExpressionSet.
GeneSetCollection class: GeneSetCollection.
agdex
; write.agdex.result
; agdex.scatterplot
;
get.gset.result.details
; read.agdex.gset.details
; read.agdex.gset.details
;
# load data data(human.data) data(mouse.data) data(gset.data) # make dex.set object for human data dex.set.human <- make.dex.set.object(human.data, comp.var=2, comp.def="human.tumor.typeD-other.human.tumors", gset.collection=gset.data) # make dex.set object for mouse data dex.set.mouse <- make.dex.set.object(mouse.data, comp.var=2, comp.def="mouse.tumor-mouse.control", gset.collection=NULL)