PWAmat {annotate}R Documentation

A function to compute the probe to KEGG pathway incidence matrix.

Description

For a given chip we compute the mapping from probes to KEGG pathways.

Usage

PWAmat(data)

Arguments

data The name of the chip for which the incidence matrix should be computed.

Details

Not much to say, just find which probes are in which pathways and return the incidence matrix, with pathways as rows and probes as columns.

It would be nice to be able to specify a set of probes to use, so that one does not do perform the calculations using all probes if they are not of interest.

Value

A matrix containing zero or one, depending on whether the probe (column) is in a pathway (row).

Author(s)

R. Gentleman

See Also

KEGG2heatmap, GOmnplot

Examples

  if(require("hgu95av2") ) {
    Am1 = PWAmat("hgu95av2")
 }

[Package annotate version 1.8.0 Index]