geneModelFromTxdb: Prepare gene model from an object of TxDb

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

Prepare gene model from an object of TxDb

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

Generate a list of track from a TxDb object.

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="-")

jianhong/trackViewer documentation built on Nov. 10, 2024, 10:33 a.m.