spliceSites-package: Calculate information on splice-sites from gapped alignments...

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from 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 <[e-mail]>

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

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.