binGenome: Feature coordinates extraction
In ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description Usage Arguments Details Value Author(s) See Also Examples

Exons and introns are subdivided into new features called exon and intron bins and are then classified into exclusively exonic bins, exclusively intronic bins or alternative splicing (AS) bins .

1	binGenome(genome, geneSymbols, logTo = "ASpli_binFeatures.log" )

`genome`	An object of class transcriptDb (TxDb)
`geneSymbols`	A dataframe with symbol (common names) of TxDb genes. If geneSymbols is NULL, gene name will be repeated
`logTo`	Filename where to print features extraction log

Exon and intron coordinates are extracted from gene annotation, only those from multi-exonic genes are saved for further evaluation. In case more than one isoform exist, some exons and introns will overlap. Exons and introns are then disjoint into new features called exon and intron bins, and then they are classified into exclusively exonic bins, exclusively intronic bind or alternative splicing bins (AS-bins), which are labeled according to which alternative splicing event are assumed to came from:

ES: exon skipping
IR: intron retention
Alt5|3'ss: alternative five/three prime splicing site
"*" (ES*, IR*, AltSS*) means this AS bin/region is involved simultaneously in more than one AS event type
external: from the beginning or the end of a transcript

Subgenic features are labeled as follow (hypothetical GeneAAA):

GeneAAA:E001: defines first exonic bin
GeneAAA:I001: defines first intronic bin
GeneAAA:Io001: defines first intron before disjoint into bins
GeneAAA:J001: defines first junction

Junctions are defined as the last position of five prime exon (donor position) and first position of three prime exon (aceptor position). Using TxDb object, it is possible to extract annotated/known junctions. This information will be useful for the analysis of "experimental" junctions (reads aligned with gaps). Bins and junctions are labelled always in 5' to 3' sense. This notation is strand independent. It implies that bin / junction with lower numbering is always at 5'.

An ASpliFeatures object. It is a list of features using GRanges format.

Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

featuresg, featuresb, featuresj

  # Create a transcript DB from gff/gtf annotation file.
  library(GenomicFeatures)
  gtfFileName <- aspliExampleGTF()
  genomeTxDb <- makeTxDbFromGFF( gtfFileName )
  
  # Create an ASpliFeatures object from TxDb
  features <- binGenome( genomeTxDb )

  # Extract gene, bin and junctions features
  GeneCoord <- featuresg(features)
  BinCoord <- featuresb(features)
  JunctionCoord <- featuresj(features)