firma.score: Get Splice Score from FIRMA
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Extracts the FIRMA splice score from data.frame data.

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firma.score(xps.data,
            probeset = NULL,
            option   = "probeset")

`xps.data`	object of class `ExprTreeSet`.
`probeset`	probesetID or NULL.
`option`	option determining the `probeset` type for which to extract expression levels, one of ‘probeset’, ‘exon’.

Function firma.score returns the FIRMA splice score described in Purdom et al. from slot data for a given probeset, or for all probesets in case of probeset=NULL. Row names will be the Affymetrix probesetIDs or exonIDs, respectively, dependent on the selected option.

A data.frame.

For option="probeset" parameter probeset should usually be the transcriptID in order to get the splice scores for all probesetIDs of the corresponding transcriptID.

Christian Stratowa

Purdom, E., Simpson K.M., Robinson M.D., Conboy J.G., Lapuk A.V. and Speed, T.P. (2008), FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 24(15):1707-1714

firma

## Not run: 
## get probeset splice scores for all probeset or for probeset=2429278
score.firma <- firma.score(sub.firma.ps, probeset=NULL, option="probeset")
score.firma <- firma.score(sub.firma.ps, probeset=2429278, option="probeset")

## get probeset splice scores for all probesets corresponding to transcript=2429277
score.firma <- firma.score(sub.firma.ps, probeset=2429277, option="probeset")

## End(Not run)