aggregateExprs: Aggregate expression data

In PGSEA: Parametric Gene Set Enrichment Analysis

Description

This function removes duplicates row names from an expression set, summarizing them with a function of the users choice. The "absMax" function located in package "reb" we have found to be useful.

Usage

aggregateExprs(x, package = "hgu133plus2", using = "ENTREZID", FUN, ...)

Arguments

x	expression data - matrix, eSet, or ExpressionSet
package	annotation package of expression data
using	format type that gene IDs are converted to
FUN	function by which to summarize duplicated values
...	extra parameters passed on to FUN

Value

A matrix of expression data with the rows aggregated to a unique format chosen by the user. The new identifiers of the returned matrix are those specified with the "using" argument. To see possible values, use the ls() command illustrated below in the examples.

Author(s)

Kyle Furge <[e-mail]> and Karl Dykema <[e-mail]>

Examples

	if (require(hgu95av2.db) & require(annaffy)) {
		library(annaffy)
		data(aafExpr)
		class(exprs(aafExpr))
		exprs(aafExpr)[1:4, 1:4]

		#list possible values for the "using" argument
		ls(pos=which(search()=="package:hgu95av2.db"))

		convert <- aggregateExprs(exprs(aafExpr),"hgu95av2.db",FUN=mean,na.rm=TRUE)
		convert[1:4,1:4]
	}

PGSEA documentation built on April 28, 2020, 8:28 p.m.