writeFastaSA {sangeranalyseR} | R Documentation

## Method writeFastaSA

### Description

Method writeFastaSA

### Usage

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

### Arguments

`object` | A 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 value can be `all`, `contigs_alignment`, `contigs_unalignment` or `all_reads`. It generates reads and contigs FASTA files.

### Value

The output directory of FASTA files.

### Examples

    data(sangerAlignmentData)
    writeFastaSA(sangerAlignmentData)

[Package sangeranalyseR version 1.2.0 Index]