pathRender (version 1.40.0)

reduceES: collapse the assay values in an ExpressionSet to a set of specified genes, using a statistic when multiple probes map to a given gene

Description

collapse the assay values in an ExpressionSet to a set of specified genes, using a statistic when multiple probes map to a given gene

Usage

reduceES(es, annovec, ann2featMap, pdvname="symbol", collapseFun=NULL)

Arguments

es

ExpressionSet instance

annovec

genes to retain

ann2featMap

either an AnnDbBimap from AnnotationDbi (typically constructed with revmap(), or a named vector mapping from symbols to probe set IDs

pdvname

featureData variable name to be used to hold the annotations of variables kept

collapseFun

statistical function for collapsing data across probes mapping to the same gene

Value

An ExpressionSet instance limited to genes in annovec, condensed if necessary using collapseFun to get one number per gene from multiple probes

Examples

library(ALL)
data(ALL)
library(hgu95av2.db)
rr = revmap(hgu95av2SYMBOL)
exprs(reduceES(ALL[,1:3], c("BCL2", "CPNE1"), rr, "sym", mean))