Prepare gene model from an object of TxDb

Share:

Description

Generate an object of track for viewTracks by given parameters.

Usage

1
2
3
4
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

Author(s)

Jianhong Ou

See Also

See Also as importScore, importBam, viewTracks

Examples

1
2
3
4
5
6
7
8
    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="-")