trackViewer (version 1.8.3)

geneModelFromTxdb: 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

• 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="-")