writeFasta {sangeranalyseR} | R Documentation

## Method writeFasta

### Description

A method which writes FASTA files of the SangerRead, SangerContig, and SangerAlignment instance.

### Usage

    writeFasta(object, outputDir = NULL, compress = FALSE,
      compression_level = NA, selection = "all")

### Arguments

`object` | A SangerRead, SangerContig, or SangerAlignment S4 instance.
`outputDir` | The output directory of generated FASTA files.
`compress` | Like for the `save` function in base R, must be `TRUE` or `FALSE` (the default), or a single string specifying whether writing to the file is to use compression. The only type of compression supported at the moment is "gzip". This parameter will be passed to `writeXStringSet` function in Biostrings package.
`compression_level` | This parameter will be passed to `writeXStringSet` function in Biostrings package.
`selection` | This parameter will be passed to `writeFastaSC` or `writeFastaSA`.

### Value

A `SangerRead`, `SangerContig`, or `SangerAlignment` object.

### Author(s)

Kuan-Hao Chao

### Examples

    data(sangerReadFData)
    data(sangerContigData)
    data(sangerAlignmentData)
    ## Not run:
    writeFasta(sangerReadFData)
    writeFasta(sangerContigData)
    writeFasta(sangerAlignmentData)
    ## End(Not run)

[Package sangeranalyseR version 1.2.0 Index]