CMAPCollection-class: Class '"CMAPCollection"'

In gCMAP: Tools for Connectivity Map-like analyses

Description

An extension of the eSet class for the efficient storage of (large) gene set collections.

Objects from Class CMAPCollection

Objects can be created by calls of the form new("CMAPCollection", assayData, phenoData, featureData, experimentData, annotation, protocolData, ...). Alternatively, the user-friendly 'CMAPCollection' method is available.

The induceCMAPCollection function can be used to apply thresholds to numerical scores stored in eSet-like objects and returns a CMAPCollecion (see examples).

The CMAPCollection class is derived from the virtual eSet class. The assayData slot contains information about the membership of genes (rows) in gene sets (columns) in the form of an incidence matrix. The incidence matrix, accessible through the 'members' method, is a 'sparseMatrix' object, in which 1 / -1 entries identify gene set membership of up- and downregulated genes, respecively.

As opposed to the well-established GeneSetCollection class defined in the GSEABase package, the CMAPCollection class stores gene set membership in a matrix format, allowing direct access to individual gene sets as well as the relationships between different sets. The incidence matrix offers memory efficient storage of large gene set collection and can directly be used in matrix-based gene set analyses.

Through direct extension of the virtual eSet class, featureData and phenoData slots are available for storage of gene- and gene-set annotation, respectively. The column 'signed' in the phenoData slot indicates whether the different gene sets ( columns ) should be considered to be signed to disambiguate cases in which all gene set members are identified by a +1 entry. In this case, 'signed' = TRUE indicates that these genes should be considered upregulated members of the set (and no down-regulated members were identified / stored). If 'signed' = FALSE, no information about directionality is available, e.g. gene set members can be either up- or downregulated.

Slots

assayData:

Object of class "AssayData"

phenoData:

Object of class "AnnotatedDataFrame"

featureData:

Object of class "AnnotatedDataFrame"

experimentData:

Object of class "MIAxE"

annotation:

Object of class "character"

protocolData:

Object of class "AnnotatedDataFrame"

.__classVersion__:

Object of class "Versions"

Extends

Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.

Methods

geneIds

signature(object = "CMAPCollection"): Returns a list of gene identifiers, with one list entry for each column of the assayDataSlot 'members'.

members

signature(object = "CMAPCollection"): Returns the number of gene members in each gene set stored in the collection. For signed sets, also the number of up-/down-regulated members is returned.

members

signature(object = "CMAPCollection"): Returns the coincidence matrix as stored in the assayData slot of the CMAPCollection as a sparseMatrix object (rows=genes, columns=gene sets).

signed

signature(object = "CMAPCollection"): Returns the 'signed' column of the phenoData slot, indicating whether gene sets should be considered signed (TRUE) or un-signed (FALSE).

signed<-

signature(x = "CMAPCollection"): Replacement method for the 'signed' column of phenoData.

minSetSize

signature(sets = "CMAPCollection"): Filter CMAPcollection for minimum number of set members.

incidence

signature(x = "CMAPCollection"): Returns in the transpose of the coincidence matrix stored in the assayData slot, mirroring the definition of 'incidence' for GeneSetCollections as defined in the GSEABase package.

mergeCollections

signature(x = "CMAPCollection", y = "CMAPCollection"): Combines two CMAPCollections into one.

upIds

signature(x = "CMAPCollection"): Returns the gene identifiers of all up-regulated gene set members (sign = 1).

downIds

signature(x = "CMAPCollection"): Returns the gene identifiers of all down-regulated gene set members (sign = -1).

Note

The CMAPCollections class supports coercion from / to GeneSet and GeneSetCollection objects defined by the GSEABase package, as well as the SignedGeneSet derivative introduced by the gCMAP package itself.

Author(s)

Thomas Sandmann, [e-mail]

See Also

induceCMAPCollection, GeneSetCollection, SignedGeneSet

Examples

## empty CMAPCollection
new("CMAPCollection")

## CMAPCollection from matrix
mat <- matrix( sample( c(-1,0,1), 100, replace=TRUE), ncol=10)
cmap <- CMAPCollection( mat )
members( cmap )

## CMAPCollection induced from NChannelSet
data( gCMAPData )
assayDataElementNames( gCMAPData )

cmap <- induceCMAPCollection(gCMAPData, "z", lower=-2, higher=2)
cmap
setSizes( cmap )
pData(cmap)
signed(cmap) <- c(TRUE, FALSE, TRUE)
signed(cmap)
head(members(cmap))

out <- fisher_score(cmap[,1], cmap, universe = featureNames( cmap))
out

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