DeconGeneSetCollection: Collection of cell- or tissue-specific gene sets

Description Usage Arguments Value See Also Examples

Description

Classes used for collections of cell- or tissue-specific gene sets for use in deconvolution, along with specialized accessor functions. The primary use for this class is the use of a specialized incidence function, and some slightly improved mapping capabilities.

Usage

1
2
3
4
5
6
7
    DeconGeneSetCollection(object, idType = EntrezIdentifier(), 
        setType = DeconCollection())
    
    description(object, ...)
    description(object) <- value
    
    collectionType(object) <- value

Arguments

object

A GeneSetCollection, or any other object that can be coerced to a GeneSetCollection using the constructor for that class.

idType

An argument of class ‘GeneIdentifierType’, used to indicate how the ‘geneIds’ will be represented.

setType

An argument of class ‘CollectionType’, used to indicate what kind of collection is created. Defaults to IRISCollection, the default class for cell type specific gene sets.

value

For description, a character vector as long as the number of GeneSets in the collection, for collectionType, a vector of CollectionTypes as long as the number of GeneSets in the collection

...

Further arguments to be passed on to other methods.

Value

For DeconGeneSetCollection, an object of class DeconGeneSetCollection with geneIds from the appropriate geneIdType. The gene sets in the collection represent genes that are relatively specific to that particular tissue or cell type. For description, a character vector with the description from each of the GeneSets in the collection.

See Also

DeconCollection-class, GeneSetCollection-class

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
    
    ## Get a set of tissue specific marker genes.
    dgsc <- DeconGeneSetCollection()
    
    ### Get the descriptions from the collection
    description(dgsc)
    
    ### Make a normal GeneSetCollection
    gs1 <- GeneSet(setName = "Set1", shortDescription = "Example 1")
    gs2 <- GeneSet(setName = "Set2", shortDescription = "Example 2")
    gsc2 <- GeneSetCollection(list(gs1, gs2))
    ### Coerce it to a DeconGeneSetCollection
    dgsc2 <- DeconGeneSetCollection(gsc2)
    dgsc2
    
    ### Map them to a popular microarray platform
    library(hgu133plus2.db)
    u133GSC <- mapIdentifiers(dgsc, AnnotationIdentifier(), hgu133plus2ENTREZID)

JasonHackney/GSDecon documentation built on Dec. 2, 2018, 1:12 p.m.