SangerAlignment-class-writeFastaSA: writeFastaSA

In sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

Description

A SangerAlignment method which writes sequences into Fasta files.

Usage

## S4 method for signature 'SangerAlignment'
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)

sangeranalyseR documentation built on Nov. 8, 2020, 5:59 p.m.