R: Class '"geneList"'

geneList-class {refGenome} | R Documentation

## Class `"geneList"`

### Description

geneList represents data for a single gene.

### Usage

    geneList(ref, genes, interior=TRUE)

### Arguments

`ref` | ensemblGenome or ucscGenome. Genome object from which gene data is extracted.

`genes` | Vector of gene_id's

`interior` | When `FALSE`, exon and transcript data skipped.

### Objects from the Class

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

### Slots

`l`:

  Object of class `"list"`. List containing `geneModel` objects.

### Methods

show

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

length

  `signature(object= "geneList"` Returns length of contained (geneModel) list.

names

  `signature(object= "geneList"` Returns names of contained (geneModel) list.

names<-

  `signature(object= "geneList",i="numeric"` Sets names of contained (geneModel) list.

+

  `signature(e1= "geneList", e2="geneList"` Combines two lists together.

### Author(s)

Wolfgang Kaisers

### Examples

    ##-------------------------------------##
    ## A) Ensembl
    ##-------------------------------------##
    ensfile <- system.file("extdata",
                            "hs.ensembl.62.small.RData", package="refGenome")
    ens <-loadGenome(ensfile)
    gt <- getGeneTable(ens)
    gl <- geneList(ens, gt$gene_id, interior=TRUE)
    names(gl)
    length(gl)
    gl
    gl[1]
    gl[1] + gl[2]

[Package refGenome version 1.7.7 Index]