splicegear (version 1.44.0)

SpliceSitesGenomic-class: Class "SpliceSitesGenomic"

Description

A class to store alternative splicing information on a genomic point of view.

Objects from the Class

Objects can be created by calls of the form new("SpliceSitesGenomic", seq, seq.length, spsiteIpos, spsiteIIpos, spsiteIIIpos, spsiteIpos.pData, spsiteIIpos.pData, spsiteIIIpos.pData, ...).

Slots

variants:

Object of class "list". There is one element per splice variant. Each element in the list should be a vector of integers. Each integer refers to an exon. The sequence of integers determines the sequence of exons in the splice variant.

seq:

Object of class "character", from class "SpliceSites".

seq.length:

Object of class "integer", from class "SpliceSites".

spsiteIpos:

Object of class "matrix", from class "SpliceSites".

spsiteIIpos:

Object of class "integer", from class "SpliceSites". This should not have any practical use in this class.

spsiteIIIpos:

Object of class "matrix", from class "SpliceSites". This should not have any practical use in this class.

spsiteIpos.pData:

Object of class "AnnotatedDataFrame", from class "SpliceSites".

spsiteIIpos.pData:

Object of class "AnnotatedDataFrame", from class "SpliceSites". This should not have any practical use in this class.

spsiteIIIpos.pData:

Object of class "AnnotatedDataFrame", from class "SpliceSites". This should not have any practical use in this class.

Extends

Class "SpliceSites", directly.

Methods

plot

signature(x = "SpliceSitesGenomic", y = "missing"): a plotting method for demonstration purposes.

See Also

SpliceSites-class and plot.SpliceSitesGenomic.

Examples

## a 10 bp window
seq.length <- as.integer(10)
## positions of the exons
spsiteIpos <- matrix(c(1, 3.5, 5, 9, 3, 4, 8, 10), nc=2)
## known variants
variants <- list(a=c(1,2,3,4), b=c(1,2,3), c=c(1,3,4))

spvar <- new("SpliceSitesGenomic", spsiteIpos=spsiteIpos,
         variants=variants, seq.length=seq.length)

plot(spvar)