annotatedGenome-class: Class "annotatedGenome"
In casper: Characterization of Alternative Splicing based on Paired-End Reads

The annotatedGenome class stores info about transcripts, usually created with procGenome from TxDb objects or user-provided .gtf files.

Objects are typically created with a call to procGenome (for known genomes) or to createDenovoGenome (for de novo genomes).

islands: GRangesList object with elements corresponding to gene islands. It indicates the start/end/name of each exon contained in the island
transcripts: Each element in the list corresponds to a gene island. It indicates the exons contained in each known variant.
exon2island: data.frame indicating the chromosome, start and end of each exon, and its corresponding gene island.
exonsNI: GRanges indicating the chromosome, start/end and id of each exon
aliases: data.frame indicating the aliases for each known transcript, i.e. transcripts having the exact same sequence of exons.
genomeVersion: Character indicating the genome version from which the object was build, e.g. "hg19"
dateCreated: Character indicating the date when the object was created. UCSC genomes chance from time to time, so that an "hg19" genome from Jan 2012 may not be exactly the same as in Dec 2012.
denovo: Logical variable. FALSE indicates that the object was created using available annotation only. TRUE indicates that new exons/islands were added based on the data observed in a particular RNA-seq experiment.
txLength: Numeric vector storing transcript lengths.
knownVars: List where each element corresponds to an island, and contains a character vector with names of isoforms that should be considered as known (i.e. always included in the model)