u1_gen: Generating Data Structure

In cubfits: Codon Usage Bias Fits

Description

These utility functions generate and summarize sequence strings into several useful formats such as reu13.df, y, and n, etc.

Usage

  gen.reu13.df(seq.string, phi.df = NULL, aa.names = .CF.GV$amino.acid,
               split.S = TRUE, drop.X = TRUE, drop.MW = TRUE,
               drop.1st.codon = TRUE)
  gen.y(seq.string, aa.names = .CF.GV$amino.acid,
        split.S = TRUE, drop.X = TRUE, drop.MW = TRUE)
  gen.n(seq.string, aa.names = .CF.GV$amino.acid,
        split.S = TRUE, drop.X = TRUE, drop.MW = TRUE)

  gen.reu13.list(seq.string, aa.names = .CF.GV$amino.acid,
                 split.S = TRUE, drop.X = TRUE, drop.MW = TRUE,
                 drop.1st.codon = TRUE)
  gen.phi.Obs(phi.df)
  gen.scuo(seq.string, aa.names = .CF.GV$amino.acid,
           split.S = TRUE, drop.X = TRUE, drop.MW = TRUE)

Arguments

seq.string	a list of sequence strings.
phi.df	a phi.df object returned from read.phi.df().
aa.names	a vector contains amino acid names for analysis.
split.S	split amino acid 'S' if any.
drop.X	drop amino acid 'X' if any.
drop.MW	drop amino acid 'M' and 'W' if any.
drop.1st.codon	if drop the first codon.

Details

These functions mainly take inputs of sequence strings seq.string or phi.df and turn them into corresponding format.

Value

The outputs are data structure in corresponding formats. See AllDataFormats for details.

Author(s)

Wei-Chen Chen [e-mail].

References

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

See Also

AllDataFormats, read.seq(), read.phi.df(), and 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)
reu13.df <- gen.reu13.df(seq.string, phi.df, aa.names)
reu13.list.new <- gen.reu13.list(seq.string, aa.names)
y <- gen.y(seq.string, aa.names)
n <- gen.n(seq.string, aa.names)
scuo <- gen.scuo(seq.string, aa.names)

# Convert to list format.
reu13.list <- convert.reu13.df.to.list(reu13.df)
y.list <- convert.y.to.list(y)
n.list <- convert.n.to.list(n)

## End(Not run)

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