R: Class '"transcriptModel"'

transcriptModel-class {refGenome} | R Documentation

## Class `"transcriptModel"`

### Description

transcriptModel represents data for a single gene.

### Objects from the Class

Objects can be created by calls of the form `.transcriptModel()`.

### Slots

`id`:

  Object of class `"character"`. ID of one single transcript.

`name`:

  Object of class `"character"`. Name of one single transcript.

`gene_id`:

  Object of class `"character"`. ID of one single gene.

`gene_name`:

  Object of class `"character"`. Name of one single gene.

`seq_name`:

  Object of class `"character"`. Name of sequence (chromosome).

`strand`:

  Object of class `"character"`. Strand of one gene.

`biotype`:

  Object of class `"character"`. Biotype of transcript.

`coords`:

  Object of class `"character"`. Limiting coordinates (start, end) of gene.

`exons`:

  Object of class `"data.frame"` with two columns. Contains limiting coordinates (start, end) of exons.

`cds`:

  Object of class `"data.frame"` with two columns. Contains limiting coordinates (start, end) of CDS.

`stcodon`:

  Object of class `"integer"`. Coordinates start and stop codons.

`prime_utr`:

  Object of class `"integer"`. Coordinates five- and three-prime_utr.

`version`:

  Object of class `"integer"`. Version as stated in ensembl GTF files.

### Methods

show

  `signature(object = "transcriptModel")`: Creates a sensible printout.

### Author(s)

Wolfgang Kaisers

### Examples

    ##-------------------------------------##
    ## A) Ensembl
    ##-------------------------------------##
    ensfile <- system.file("extdata",
                            "hs.ensembl.62.small.RData", package="refGenome")
    ens <- loadGenome(ensfile)

    gt <- getGeneTable(ens)
    gene_id <- as.character(gt$gene_id[1])
    gm <- geneModel(ens, gene_id)
    tr <- getTranscript(gm, 1)
    tr
    getExonData(tr)
    getCdsData(tr)
    ##-------------------------------------##
    ## B) UCSC
    ##-------------------------------------##
    ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(ucfile)
    gt <- getGeneTable(uc)
    gene_id <- as.character(gt$gene_id[1])
    gm <- geneModel(uc, gene_id)
    tr <- getTranscript(gm, 1)
    tr

[Package refGenome version 1.7.7 Index]