GenomicFeatures: makeTxDbFromGRanges – R documentation

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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

A TxDb object.

Author(s)

Hervé Pagès

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

GenomicFeatures

Conveniently import and query gene models

v1.42.3

Artistic-2.0

Authors

M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence, V. Obenchain

Initial release