probe2gene {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

    probe2gene(
      probeSE,
      chip = NA,
      from = "PROBEID",
      to = "ENTREZID",
      multi.to = "first",
      multi.from = "mean"
    )

### Arguments

`probeSE` | Probe expression data. An object of class `SummarizedExperiment`. Make sure that the `metadata` contains an element named `annotation` that provides the corresponding ID of a recognized platform such as `hgu95av2` (Affymetrix Human Genome U95 chip). This requires that a corresponding `.db` package exists (see http://www.bioconductor.org/packages/release/BiocViews.html#___ChipName for available chips/packages) and that you have it installed. Alternatively, the mapping from probe to gene can also be defined in the `rowData` slot via two columns named (i) `PROBEID` for the platform-specific probe ID, and (ii) `ENTREZID` for the corresponding NCBI Entrez Gene ID.
`chip` | Character. The ID of a recognized microarray platform. Only required if not provided in the `metadata` of `probeSE` via an element named `annotation`.
`from` | Character. ID type from which should be mapped. Corresponds to the ID type of the names of argument `se`, with the default `PROBEID` being appropriate if the mapping is based on Bioconductor annotation packages. Note that `from` is ignored if `to` is a `rowData` column of `probeSE`.
`to` | Character. Gene ID type to which should be mapped. Corresponds to the gene ID type the rownames of argument `probeSE` should be updated with. Note that this can also be the name of a column in the `rowData` slot of `probeSE` to specify user-defined mappings in which conflicts have been manually resolved. Defaults to `ENTREZID`.
`multi.to` | How to resolve 1:many mappings, i.e. multiple gene IDs for a single probe ID? This is passed on to the `multiVals` argument of `mapIds` and can thus take several pre-defined values, but also the form of a user-defined function. However, note that this requires that a single gene ID is returned for each probe ID. Default is `"first"`, which accordingly returns the first gene ID mapped onto the respective probe ID.
`multi.from` | How to resolve many:1 mappings, i.e. multiple probe IDs mapping to the same gene ID? Pre-defined options include: 'mean' (Default): updates the respective gene expression with the average over the expression of all probes mapping to that gene, 'first': returns the first probe ID for each gene ID with multiple probe IDs, 'minp' selects the probe ID with minimum p-value (according to the `rowData` column `PVAL` of `probeSE`), 'maxfc' selects the probe ID with maximum absolute log2 fold change (according to the `rowData` column `FC` of `probeSE`).

### Value

A `SummarizedExperiment` on gene level.

### Author(s)

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

### See Also

`readSE` for reading expression data from file, `deAna` for differential expression analysis.

### Examples

        # (1) reading the expression data from file
        exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
        cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
        rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
        probeSE <- readSE(exprs.file, cdat.file, rdat.file)
        geneSE <- probe2gene(probeSE)

[Package EnrichmentBrowser version 2.20.7 Index]