R: Class '"refExons"'

refExons-class {refGenome} | R Documentation

## Class `"refExons"`

### Description

refExons represents genomic annotation data on exon-features for Ensembl and UCSC genomes. Relative locations of CDS, start_codon and stop_codon features are added. The unifiedExons class is intended to be used as preparation of exonic coordinates for counting of alignments (reads) inside these regions. In order to prevent ambiguities, overlaps are removed.

### Objects from the Class

Objects can be created by calls of the form `refExons(rg)`. 'rg' represents an object of class `ensemblGenome` or `ucscGenome`.

### Slots

`basedir`:

  Object of class `"character"` Directory where SQLite database is written.

`ev`:

  Object of class `"environment"` Environment that contains data structures. Optionally, there are gtf and attr data.frames.

### Methods

show

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

getSpliceTable

  `signature(object = "ensemblExons", coding="logical")`: Returns tabled splice sites. When `coding`=TRUE only entries with `gene_biotype=="protein_coding"` are included.

### Author(s)

Wolfgang Kaisers

### References

Ensembl File index

  http://www.ensembl.org/info/data/ftp/index.html

GTF Field definitions

  http://mblab.wustl.edu/GTF22.html#fields

UCSC home page

  http://genome.ucsc.edu/

### Examples

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

    saveGenome(enex,"enex.RData", useBasedir=FALSE)
    er <- loadGenome("enex.RData")

    # Unify exons
    uex <- unifyRanges(enex)

    ##-------------------------------------##
    ## B) UCSC
    ##-------------------------------------##
    ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(ucfile)
    ucex <- refExons(uc)

    saveGenome(ucex, "ucex.RData", useBasedir=FALSE)
    ur <- loadGenome("ucex.RData")

[Package refGenome version 1.7.7 Index]