writeFasta: Method writeFasta

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

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)

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