reduceES: collapse the assay values in an ExpressionSet to a set of...
In pathRender: Render molecular pathways

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

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

`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

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

Vince Carey <stvjc@channing.harvard.edu>

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

pathRender documentation built on Nov. 8, 2020, 8:03 p.m.

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