probe.2.gene.eset {EnrichmentBrowser}R Documentation

Transformation of probe level expression to gene level expression

Description

Transforms expression data on probe level to gene level expression by summarizing all probes that are annotated to a particular gene.

Usage

    probe.2.gene.eset( probe.eset, use.mean = TRUE )

Arguments

probe.eset

Probe expression data of class SummarizedExperiment. The rowData slot of the expression dataset must contain a 'GENE' column that lists for each probe the corresponding KEGG gene ID.

use.mean

Logical. Determining, in case of multiple probes for one gene, whether a mean value is computed (use.mean=TRUE), or the probe that discriminate the most between the two sample group is kept (use.mean=FALSE). Defaults to TRUE.

Value

A SummarizedExperiment on gene level.

Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

See Also

read.eset for reading expression data from file, de.ana for differential expression analysis.

Examples

    # (1) reading the expression data from file
    exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
    pdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
    fdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
    probe.eset <- read.eset(exprs.file, pdat.file, fdat.file)
    gene.eset <- probe.2.gene.eset(probe.eset) 

[Package EnrichmentBrowser version 2.8.7 Index]