mapByVar: Select probeset by variance and get PPI ID

In assaron/BioNet: Routines for the functional analysis of biological networks

Description

The function selects for each gene the probeset with the highest variance and gets the PPI ID for each gene. The PPI identifier is: gene symbol(Entrez ID). Affymetrix identifiers are mapped to the ENTREZ ID.

Usage

mapByVar(exprSet, network=NULL, attr="geneID", ignoreAFFX=TRUE)

Arguments

exprSet	Affymetrix ExpressionSet.
network	Network that is used to map the Affymetrix identifiers.
attr	The attribute of the network that is used to map the Affymetrix IDs. The IDs are mapped to the unique Entrez gene IDs, which are by default stored in the "geneID" attribute of the network.
ignoreAFFX	Boolean value, whether to ignore or leave AFFX control genes.

Value

Expression matrix with one gene (PPI ID) per probeset.

Author(s)

Daniela Beisser

Examples

## Not run: library(ALL);
data(ALL);
mapped.e.set <- mapByVar(ALL);
mapped.e.set[1:10,];
## End(Not run)

assaron/BioNet documentation built on Sept. 18, 2020, 12:02 a.m.