summarize.miR {ExiMiR} | R Documentation

## ExiMiR low-level function for summarization.

### Description

This function performs summarization on an `AffyBatch` object using a GAL or CDF annotation environment and generates an `ExpressionSet` object containing the results.

### Usage

    summarize.miR(abatch,
    	      pmcorrect.method='pmonly',
    	      pmcorrect.param=list(),
    	      summary.method='medianpolish',
    	      summary.param=list(),
    	      summary.subset=NULL)

### Arguments

`abatch` | An `AffyBatch` object.
`pmcorrect.method` | Character vector. It contains the name of the PM correction method, which is enabled only when numerical values are available for the MM probes of the input `AffyBatch` object. Running `NormiR.pmcorrect.methods(abatch)` indicates which other methods can be chosen instead of the default one `pmonly`.
`pmcorrect.param` | A `R` list of optional parameters for the selected `pmcorrect.method`, as specified in the documentation of the original function `pmcorrect` function of the `affy` package.
`summary.method` | Character vector. It contains the name of the summarization method. Running `NormiR.summary.methods()` indicates which other methods can be chosen instead of the default one `medianpolish`.
`summary.param` | A `R` list of optional parameters for the selected `summary.method`, as specified in the documentation of the original `AffyBatch` method `computeExprSet` contained in the `affy` package.
`summary.subset` | A `R` list of probe set identifiers. When left to its default `NULL` value, the summarized expression values are computed for all probe sets available on the array.

### Value

An `ExpressionSet` containing the summarized expression data.

### Author(s)

Sylvain.Gubian, Alain Sewer, PMP SA

### See Also

`NormiR.pmcorrect.methods`, `NormiR.summary.methods`, `NormiR`.

### Examples

    data(galenv)
    data(GSE20122)
    eset <- summarize.miR(GSE20122,
                          summary.method="medianpolish")

[Package ExiMiR version 2.29.1 Index]