plotTxModelsOLD: Plot transcripts stored in a TxDB.

In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data

Description

Plot the transcript models of a gene.

Usage

plotTxModelsOLD(
  db = NULL,
  g = NULL,
  tid = NULL,
  addChevrons = T,
  rangex = NULL
)

Arguments

db	A TxDb containing transcript models from Ensembl.
g	If the TxDb contains more than one gene, then use g to specify what to plot.
addChevrons	Boolean indicating wheter to add chevrons to intronic regions to indicate direction of the transcript.
rangex	The range in genomic coordinates for the region of interest. This is important for correct alignment of the tx model plot with splice junction plot.
ex	GrangesList with exonsBy tx.
int	GrangesList with intronsByTranscript information.

Value

Don't know?

Examples

ensembl <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
annot <- getBM(
  attributes = c("ensembl_gene_id", "external_gene_name", "ensembl_transcript_id", "external_transcript_name", "transcript_tsl", "chromosome_name", "start_position", "end_position", "strand"),
  filters = "external_gene_name",
  values = "FIRRE",
  mart = ensembl
)
txdb <- makeTxDbFromBiomart(transcript_ids = annot$ensembl_transcript_id)#, host = "uswest.ensembl.org")
plotTranscripts(tdb = txdb)
Plot transcript models.

Using data stored in a TxDb to visualize the transcript models.

KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.