R: ExiMiR low-level function for summarization.

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

Examples

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

[Package ExiMiR version 2.24.0 Index]