aggregateExprs: Aggregate expression data

Description Usage Arguments Value Author(s) Examples

View source: R/PGSEA.R

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

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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 <[email protected]> and Karl Dykema <[email protected]>

Examples

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	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 May 2, 2018, 6 p.m.