u0_io: Input and Output Utility

In cubfits: Codon Usage Bias Fits

Description

These utility functions read and write data of FASTA and phi.df formats.

Usage

  read.seq(file.name, forceDNAtolower = FALSE, convertDNAtoupper = TRUE)
  write.seq(seq.data, file.name)

  read.phi.df(file.name, header = TRUE, sep = "\t", quote = "")
  write.phi.df(phi.df, file.name)

  get.expath(file.name, path.root = "./ex_data/", pkg = "cubfits")

Arguments

file.name	a file name to read or write.
forceDNAtolower	an option passed to read.fasta() of seqinr package.
convertDNAtoupper	force everything in upper case.
header	an option passed to read.table().
sep	an option passed to read.table().
quote	an option passed to read.table().
seq.data	a seq.data object.
phi.df	a phi.df object.
path.root	root path for the file name relatively to the pkg.
pkg	package name for the path of root.

Details

read.seq() and write.seq() typically read and write FASTA files (DNA ORFs or sequences).

read.phi.df() and write.phi.df() typically read and write phi.df files (expression values of ORFs or sequences).

get.expath() is only for demonstration returning a full path to the file.

Value

read.seq() returns an object of seq.data format which can be converted to seq.string format later via convert.seq.data.to.string().

read.phi.df() returns an object of phi.df format which contains expression values.

Author(s)

Wei-Chen Chen [e-mail].

References

https://github.com/snoweye/cubfits/

See Also

convert.seq.data.to.string().

Examples

## Not run: 
suppressMessages(library(cubfits, quietly = TRUE))

seq.data <- read.seq(get.expath("seq_200.fasta"))
phi.df <- read.phi.df(get.expath("phi_200.tsv"))
aa.names <- c("A", "C", "D")

# Read in from FASTA file.
seq.string <- convert.seq.data.to.string(seq.data)

## End(Not run)

Example output

Loading required package: coda
Loading required package: foreach
Loading required package: parallel

cubfits documentation built on Nov. 8, 2021, 1:07 a.m.