SpliceSitesGenomic-class: Class "SpliceSitesGenomic"

In splicegear: splicegear

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)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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