spliceSites-package {spliceSites} | R Documentation

## Calculate information on splice-sites from gapped alignments in RNA-seq data.

### Description

The package defines 'cRanges' the (centered ranges) class which represents a genomic range that contains a highlighted position (center): This will usually be the boundary between an exon and an intron. The second defined type is the class 'gapSites' which represents two exonic regions divided by a gap (usually an intron). There are subclasses which additionally contain DNA or AA sequences.

### Details

Package: | spliceSites
Type: | Package
Version: | 1.0
Date: | 2012-10-28
License: | GPL-2
Depends: | methods,rbamtools,refGenome,Biobase,BiocGenerics,Biostrings,seqLogo

### Author(s)

Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

### References

Yeo G, Burge CB Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004; 11(2-3):377-94 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

### See Also

`rbamtools` `refGenome`

### Examples

    bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
    reader <- bamReader(bam, idx=TRUE)
    ga <- alignGapList(reader)
    bamClose(reader)
    dnafile <- system.file("extdata", "dna_small.RData", package="spliceSites")
    load(dnafile)
    ucf <- system.file("extdata","uc_small_junc.RData", package="spliceSites")
    ucj <- loadGenome(ucf)
    annotation(ga) <- annotate(ga, ucj)
    ga

[Package spliceSites version 1.28.0 Index]