| SpliceSitesGenomic-class {splicegear} | R Documentation |
A class to store alternative splicing information on a genomic point of view
Objects can be created by calls of the form new("SpliceSitesGenomic", seq, seq.length, spsiteIpos, spsiteIIpos, spsiteIIIpos, spsiteIpos.pData, spsiteIIpos.pData, spsiteIIIpos.pData, ...).
variants:"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:"character", from class "SpliceSites" seq.length:"integer", from class "SpliceSites" spsiteIpos:"matrix", from class "SpliceSites" spsiteIIpos:"integer", from
class "SpliceSites". This should not have any practical use in this class.spsiteIIIpos:"matrix", from
class "SpliceSites". This should not have any practical use in this class.spsiteIpos.pData:"phenoData", from class "SpliceSites"spsiteIIpos.pData:"phenoData",
from class "SpliceSites". This should not have any practical use in this class.spsiteIIIpos.pData:"phenoData",
from class "SpliceSites". This should not have any practical use in this class.
Class "SpliceSites", directly.
signature(x = "SpliceSitesGenomic", y =
"missing"): a plotting method for demonstration purposes.
SpliceSites-class and plot.SpliceSitesGenomic.
## 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)