SignedGeneSet-class: Class '"SignedGeneSet"'

In gCMAP: Tools for Connectivity Map-like analyses

Description

A simple extension of GeneColorSet which forces geneColor to be either "down" or "up" and which ignores phenotype and phenotypeColor slots.

Objects from the Class

Construct a SignedGeneSet with the SignedGeneSet constructor method, or with a call to new. Although SignedGeneSet derives from the more abstract GeneColorSet, not phenotype argument is required; if phenotype is supplied (or is present in a template object), it will be ignored.

Slots

See GeneColorSet. No additional slots are added.

Extends

Class "GeneColorSet", directly. Class "GeneSet", by class "GeneColorSet", distance 2.

Methods

Methods specific to SignedGeneSet:

downIds

signature(object = "SignedGeneSet"): retrieve geneIds entires for which geneSign == "down".

geneSign

signature(obj = "SignedGeneSet"): alias for geneColor slot.

geneSign<-

signature(object = "SignedGeneSet", value = "character"): alias for geneColor slot, converting to factor automatically.

geneSign<-

signature(object = "SignedGeneSet", value = "factor"): alias for geneColor slot.

initialize

signature(.Object = "SignedGeneSet"): on construction, checks for appropriate geneSign/geneColor values and sets phenotype and phenotypeColor to empty strings, since these are ignored. If no geneSign/geneColor values are supplied, "up" will be used by default.

show

signature(object = "SignedGeneSet"): same as for GeneColorSet but suppresses display of unused phenotype and phenotypeColor slots.

upIds

signature(object = "SignedGeneSet"): retrieve geneIds entires for which geneSign == "up".

mapIdentifiers

signature(object = "SignedGeneSet"): Extends the 'mapIdentifiers' method implemented for GeneSets in the GSEABase package, but rejects target gene ids when multiple different (probe) identifiers with different gene signs (up / down) map to the same target.

incidence

signature(object = "SignedGeneSet") and

incidence

signature(object = "GeneSetCollection"): Mirror the 'incidence' method implemented for GeneSets in the GSEABase package, but returns sparseMatrix objects containing -1 / +1 to indicate up- and down-regulated gene members.

Examples

gene.ids <- letters[1:10]
gene.signs <- rep(c("up","down"), each=5)
SignedGeneSet(gene.ids, geneSign=gene.signs, setName="set1")

gCMAP documentation built on April 29, 2020, 3:54 a.m.