reduceES {pathRender}R Documentation

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

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

library(ALL)
data(ALL)
library(hgu95av2.db)
rr = revmap(hgu95av2SYMBOL)
exprs(reduceES(ALL[,1:3], c("DDR1", "CPNE1"), rr, "sym", mean))

[Package pathRender version 1.10.0 Index]