mapByVar: Select probeset by variance and get PPI ID

Description Usage Arguments Value Author(s) Examples

View source: R/MAUtils.R

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

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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

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

BioNet documentation built on May 2, 2018, 4:16 a.m.