summarize.miR: ExiMiR low-level function for summarization.

In ExiMiR: R functions for the normalization of Exiqon miRNA array data

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")

ExiMiR documentation built on Nov. 8, 2020, 8:26 p.m.