annotatedGenome-class {casper} | R Documentation

## Class "annotatedGenome"

### Description

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

### Objects from the Class

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

### Slots

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)

### Methods

show

  `signature(object = "annotatedGenome")`: Displays general information about the object.

### Author(s)

Camille Stephan-Otto Attolini

### See Also

`procGenome` and `createDenovoGenome` to create `annotatedGenome` objects.

### Examples

    showClass("annotatedGenome")

[Package casper version 2.24.2 Index]