geneList-class: Class '"geneList"'

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

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]

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