export-methods {BSgenome} | R Documentation

## Export a BSgenome object as a FASTA or twoBit file

### Description

`export` methods for BSgenome objects.

NOTE: The `export` generic function and most of its methods are defined and documented in the rtracklayer package. This man page only documents the 2 `export` methods define in the BSgenome package.

### Usage

    ## S4 method for signature 'BSgenome,FastaFile,ANY'
    export(object, con, format, compress=FALSE, compression_level=NA, verbose=TRUE)
    ## S4 method for signature 'BSgenome,TwoBitFile,ANY'
    export(object, con, format, ...)

### Arguments

`object` | The BSgenome object to export.
`con` | A FastaFile or TwoBitFile object. Alternatively `con` can be a single string containing the path to a FASTA or twoBit file, in which case either the file extension or the `format` argument needs to be `"fasta"`, `"twoBit"`, or `"2bit"`. Also note that in this case, the `export` method that is called is either the method with signature `c("ANY", "character", "missing")` or the method with signature `c("ANY", "character", "character")`, both defined in the rtracklayer package. If `object` is a BSgenome object and the file extension or the `format` argument is `"fasta"`, `"twoBit"`, or `"2bit"`, then the flow eventually reaches one of 2 methods documented here.
`format` | If not missing, should be `"fasta"`, `"twoBit"`, or `"2bit"` (case insensitive for `"twoBit"` and `"2bit"`).
`compress, compression_level` | Forwarded to `writeXStringSet`. See `?writeXStringSet` for the details.
`verbose` | Whether or not the function should display progress. `TRUE` by default.
`...` | Extra arguments. The method for TwoBitFile objects forwards them to `bsapply`.

### Author(s)

Michael Lawrence

### See Also

- BSgenome objects.

- The `export` generic, and FastaFile and TwoBitFile objects in the rtracklayer package.

### Examples

    library(BSgenome.Celegans.UCSC.ce2)
    genome <- BSgenome.Celegans.UCSC.ce2

    ## Export as FASTA file.
    out1_file <- file.path(tempdir(), "Celegans.fasta")
    export(genome, out1_file)

    ## Export as twoBit file.
    out2_file <- file.path(tempdir(), "Celegans.2bit")
    export(genome, out2_file)

    ## Sanity checks:
    dna0 <- DNAStringSet(as.list(genome))

    system.time(dna1 <- import(out1_file))
    stopifnot(identical(names(dna0), names(dna1)) && all(dna0 == dna1))

    system.time(dna2 <- import(out2_file))  # importing twoBit is 10-20x
                                            # faster than importing non
                                            # compressed FASTA
    stopifnot(identical(names(dna0), names(dna2)) && all(dna0 == dna2))

[Package BSgenome version 1.56.0 Index]