xps (version 1.32.0)

firma.score: Get Splice Score from FIRMA

Description

Extracts the FIRMA splice score from data.frame data.

Usage

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

Arguments

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’.

Value

A data.frame.

Details

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.

References

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

See Also

firma

Examples

## 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)