readSet: Read set of sequences.

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Reads a set of fasta files stored in folder, or a single fasta file.

Usage

readSet(folder = character(), file = character(), KOs = c(),
  zipped = FALSE, prepend.filenames = FALSE)

Arguments

folder	Path to directory containing .fasta files.
file	Path to a single .fasta file, or zipped file (if latter, specify ZIPPED = TRUE).
KOs	An optional character vector of sequence annotations (e.g. KO) contained in the names of fasta files to be selectively read.
zipped	Logical, whether folder or file is zipped. Default is FALSE.
prepend.filenames	Logical, whether to prepend filename(s) to names in DNAStringSet object. Default is FALSE.

Value

Returns a DNAStringSet object.

Examples

exampledir <- system.file("extdata", package = "coRdon")
files <- list.files(exampledir)
readSet(folder = exampledir)
readSet(folder = exampledir, KOs = "K02931")
pathtofile <- paste(exampledir, files[1], sep = "/")
readSet(file = pathtofile)

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.