spliceSites-package {spliceSites} | R Documentation |
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.
Package: | spliceSites |
Type: | Package |
Version: | 1.0 |
Date: | 2012-10-28 |
License: | GPL-2 |
Depends: | methods,rbamtools,refGenome,Biobase,BiocGenerics,Biostrings,seqLogo |
Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
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
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