Description Objects from the Class Slots Methods Author(s) Examples
transcriptModel represents data for a single gene.
Objects can be created by calls of the form
.transcriptModel()
.
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.
signature(object = "transcriptModel")
:
Creates a sensible printout.
Wolfgang Kaisers
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ##-------------------------------------##
## 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
|
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