geneModel-class: Class '"geneModel"'

In refGenome: Gene and Splice Site Annotation Using Annotation Data from 'Ensembl' and 'UCSC' Genome Browsers

Description

geneModel represents data for a single gene.

Usage

geneModel(object, gene_id, interior=TRUE)

Arguments

object

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

gene_id

One single gene_id

interior

When FALSE, exon and transcript data skipped.

Objects from the Class

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

Slots

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.

transcripts:

Object of class "character". Vector of transcript names.

coords:

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

ev:

Object of class "environment" Environment that contains data structures. Eventually contains list with transcriptModel objects.

Methods

show

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

geneId

signature(object= "geneModel" Returns (or sets) geneId (e.g. Ensembl ID).

geneName

signature(object= "geneModel" Returns (or sets) gene name (e.g. HGNC name).

getTranscript

signature(object= "geneModel",i="numeric" Returns i-th transcript object.

getTranscript

signature(object= "geneModel",i="character" Returns transcript with given name.

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, interior=TRUE)

##-------------------------------------##
## 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)
# Use "+" operator
res <- gm + gm

refGenome documentation built on May 23, 2019, 1:03 a.m.