GenomicFeatures (version 1.24.4)

makeTxDbFromGRanges: Make a TxDb object from a GRanges object

Description

The makeTxDbFromGRanges function allows the user to extract gene, transcript, exon, and CDS information from a GRanges object structured as GFF3 or GTF, and to return that information in a TxDb object.

Usage

makeTxDbFromGRanges(gr, drop.stop.codons=FALSE, metadata=NULL, taxonomyId=NA)

Arguments

gr

A GRanges object structured as GFF3 or GTF, typically obtained with rtracklayer::import().

drop.stop.codons

TRUE or FALSE. If TRUE, then features of type stop_codon are ignored. Otherwise (the default) the stop codons are considered to be part of the CDS and merged to them.

metadata

A 2-column data frame containing meta information to be included in the TxDb object. This data frame is just passed to makeTxDb, which makeTxDbFromGRanges calls at the end to make the TxDb object from the information extracted from gr. See ?makeTxDb for more information about the format of metadata.

taxonomyId

By default this value is NA which will result in an NA field since there is no reliable way to infer this from a GRanges object. But you can use this argument to supply your own valid taxId here and if you do, then the Organism can be filled in as well

Value

TxDb object.

See Also

• makeTxDbFromUCSC, makeTxDbFromBiomart, and makeTxDbFromGFF, for convenient ways to make a TxDb object from UCSC or BioMart online resources, or directly from a GFF or GTF file.

• The import function in the rtracklayer package.

• The asGFF method for TxDb objects (asGFF,TxDb-method) for the reverse of makeTxDbFromGRanges, that is, for turning a TxDb object into a GRanges object structured as GFF.

• The TxDb class.

• makeTxDb for the low-level function used by the makeTxDbFrom* functions to make the TxDb object returned to the user.

Examples

library(rtracklayer)  # for the import() function

## ---------------------------------------------------------------------
## WITH A GRanges OBJECT STRUCTURED AS GFF3
## ---------------------------------------------------------------------
GFF3_files <- system.file("extdata", "GFF3_files",
                          package="GenomicFeatures")

path <- file.path(GFF3_files, "a.gff3")
gr <- import(path)
txdb <- makeTxDbFromGRanges(gr)
txdb

## Reverse operation:
gr2 <- asGFF(txdb)

## Sanity check:
stopifnot(identical(as.list(txdb), as.list(makeTxDbFromGRanges(gr2))))

## ---------------------------------------------------------------------
## WITH A GRanges OBJECT STRUCTURED AS GTF
## ---------------------------------------------------------------------
GTF_files <- system.file("extdata", "GTF_files", package="GenomicFeatures")

## test1.gtf was grabbed from http://mblab.wustl.edu/GTF22.html (5 exon
## gene with 3 translated exons):
path <- file.path(GTF_files, "test1.gtf")
gr <- import(path)
txdb <- makeTxDbFromGRanges(gr)
txdb

path <- file.path(GTF_files, "Aedes_aegypti.partial.gtf")
gr <- import(path)
txdb <- makeTxDbFromGRanges(gr)
txdb