SpliceSites-class: Class "SpliceSites"

In splicegear: splicegear

Description

A class to store (putative) splice sites

Objects from the Class

Objects can be created by calls of the form new("SpliceSites", ...).

Slots

seq:

Object of class "character". The reference sequence.

seq.length:

Object of class "integer". The length for the reference sequence (used when the slot seq is set to "").

spsiteIpos:

Object of class "matrix". A two-columns matrix to store the begin and end positions of type I splice variant.

spsiteIIpos:

Object of class "integer". A vector to store the positions for type II splice variants.

spsiteIIIpos:

Object of class "matrix". Idem spsiteIpos, but for type III splice variants.

spsiteIpos.pData:

Object of class AnnotatedDataFrame. Used to store covariate information related to the splice variants.

spsiteIIpos.pData:

Object of class AnnotatedDataFrame.

spsiteIIIpos.pData:

Object of class AnnotatedDataFrame.

Methods

show

signature(object = "SpliceSites"): A printing method.

plot

signature(x = "SpliceSites", y = "missing"): A plotting method

Author(s)

[e-mail]

References

"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...).

See Also

isSpliceSiteOnProbe, isProbeOnSpliceSite, plot.SpliceSites, spliceset.

Examples

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)

splicegear documentation built on Oct. 31, 2019, 7:40 a.m.