SpliceSites-class {splicegear} | R Documentation |
A class to store (putative) splice sites
Objects can be created by calls of the form new("SpliceSites", ...)
.
probepos
:"matrix"
. A two-columns
matrix to store the begin and end positions of probes (one row per
probe).seq
:"character"
. The reference
sequence.seq.length
:"integer"
. The length for
the reference sequence (used when the slot seq
is set to
""
).spsiteIpos
:"matrix"
. A
two-columns
matrix to store the begin and end positions of type I splice variant.spsiteIIpos
:"integer"
. A
vector to store the positions for type II splice variants.spsiteIIIpos
:"matrix"
. Idem
spsiteIpos
, but for type III splice variants.
spsiteIpos.pData
:"phenoData"
. Used to store covariate
information related to the splice variantsspsiteIIpos.pData
:"phenoData"
spsiteIIIpos.pData
:"phenoData"
signature(object = "SpliceSites")
: A printing method. signature(x = "SpliceSites", y = "missing")
: A
plotting method laurent@cbs.dtu.dk
"Plenty of splicin' or 'can regular Affymetrix chips be used to observe alternative splicing ?'", Gautier L. et al., 2003, manuscript in preparation (and the title might have to chang...).
isSpliceSiteOnProbe
,
isProbeOnSpliceSite
,
plot.SpliceSites
,
spliceset
.
data(spliceset) print(spliceset) par(mfrow=c(1,2)) plot(spliceset, main=attr(spliceset, "name")) ## filter out supporting matches with unique positions filter.typeI <- function(x) {unique(x[duplicated(x), , drop=FALSE])} spliceset.filter <- spliceset sSites <- spliceset.filter@spliceSites sSites@spsiteIpos <- filter.typeI(sSites@spsiteIpos) spliceset.filter@spliceSites <- sSites ## plot the resulting new object plot(spliceset.filter)