refGenome (version 1.7.7)

transcriptModel-class: 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.

Examples

# NOT RUN {
##-------------------------------------##
## 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

# }