Aggregate expression data

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

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 <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>

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]
	}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PGSEA)
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: annaffy
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGSEA/aggregateExprs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: aggregateExprs
> ### Title: Aggregate expression data
> ### Aliases: aggregateExprs
> ### Keywords: datasets
> 
> ### ** 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]
+ 	}
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


            Ctrl 1   Ctrl 2   Ctrl 3   Ctrl 4
100505761 6.321550 6.087082 6.308172 6.359439
10098     2.422148 2.434130 2.668644 2.169154
10138     3.215181 3.299501 3.443626 3.364141
10277     5.748689 5.779519 5.756394 6.082581
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>