MAPAmat: Mapping chromosome bands to genes

In Bioconductor/Category: Category Analysis

Mapping chromosome bands to genes

Description

These functions return a mapping of chromosome bands to genes. makeChrBandGSC returns a GeneSetCollection object, with a GeneSet for each band. The other functions return a 0/1 incidence matrix with a row for each chromosme band and a column for each gene. Only those chromosome bands with at least one gene annotation will be included.

Usage

MAPAmat(chip, univ = NULL, minCount = 0)
makeChrBandInciMat(chrGraph)
makeChrBandGSC(chrGraph)

Arguments

chip	A string giving the annotation source. For example, "hgu133plus2"
univ	A vector of gene IDs (these should be Entrez IDs for most annotation sources). The the annotations will be limited to those in the set specified by univ. If univ is NULL (default), then the gene IDs are those found in the annotation data source.
chrGraph	A graph object as returned by makeChrBandGraph
minCount	Bands with less than minCount genes will be excluded from the returned matrix. If minCount is 0, no bands will be removed, this is the default.

Value

For makeChrBandGSC, a GeneSetCollection object with a GeneSet for each band.

For the other functions, (0/1) incidence matrix with chromosome bands as rows and gene IDs as columns. A 1 in m[i, j] indicates that the chromosome band rownames(m)[i] contains the geneID colnames(m)[j].

Author(s)

Seth Falcon, Michael Lawrence

See Also

makeChrBandGraph, cateGOry, probes2MAP

Examples

have_hgu95av2.db <- suppressWarnings(require("hgu95av2.db"))
if (have_hgu95av2.db)
   mam <- MAPAmat("hgu95av2.db")

Bioconductor/Category documentation built on Nov. 2, 2024, 6:33 a.m.