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)