makeTxDbFromGRanges: Make a TxDb object from a GRanges object

In jmacdon/GenomicFeatures: Conveniently import and query gene models

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

A TxDb object.

Author(s)

Hervé Pagès

See Also

• makeTxDbFromUCSC, makeTxDbFromBiomart, and makeTxDbFromEnsembl, for making a TxDb object from online resources.

• makeTxDbFromGFF for making a TxDb object 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 (asGFF() does not propagate the CDS phase at the moment):
target <- as.list(txdb)
target$splicings$cds_phase <- NULL
stopifnot(identical(target, 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

jmacdon/GenomicFeatures documentation built on Jan. 2, 2022, 7:40 a.m.