geneModelFromTxdb: Prepare gene model from an object of TxDb

In trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Description

Generate an object of track for viewTracks by given parameters.

Usage

geneModelFromTxdb(
  txdb,
  orgDb,
  gr,
  chrom,
  start,
  end,
  strand = c("*", "+", "-"),
  txdump = NULL
)

Arguments

txdb	An object of TxDb
orgDb	An object of "OrgDb"
gr	An object of GRanges.
chrom	chromosome name, must be a seqname of txdb
start	start position
end	end position
strand	strand
txdump	output of as.list(txdb), a list of data frames that can be used to make the db again with no loss of information.

Value

An object of track

See Also

See Also as importScore, importBam, viewTracks

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         chrom="chr20", 
                         start=22560000, 
                         end=22565000, 
                         strand="-")

trackViewer documentation built on Feb. 11, 2021, 2 a.m.