MAPAmat {Category}R Documentation

Create an incidence matrix mapping chromosome bands to genes

Description

These 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)
chrBandInciMat(chip, univ = NULL, minCount = 0)
makeChrBandInciMat(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.

Details

chrBandInciMat is a DEPRECATED alias for MAPAmat.

Value

A (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

See Also

makeChrBandGraph, cateGOry, probes2MAP

Examples

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

[Package Category version 2.10.1 Index]