makeTxDbFromGRanges {GenomicFeatures} | R Documentation

## 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

### 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

[Package GenomicFeatures version 1.40.1 Index]