binGenome {ASpli} | R Documentation

## Feature coordinates extraction

### Description

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 .

### Usage

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

### Arguments

`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
`cores` | Number of cores to use in parallel when binning the genome

### Details

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'.

### Value

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

### Author(s)

Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

### See Also

`featuresg`, `featuresb`, `featuresj`

### Examples

      # 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)

[Package ASpli version 2.4.0 Index]