Description Usage Arguments Details Value Note Author(s) References See Also Examples
Extracts the FIRMA splice score from data.frame data
.
1 2 3 | firma.score(xps.data,
probeset = NULL,
option = "probeset")
|
xps.data |
object of class |
probeset |
probesetID or NULL. |
option |
option determining the |
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
1 2 3 4 5 6 7 8 9 | ## 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)
|
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