u2_convert: Convert Data Frame to Other Formats
In cubfits: Codon Usage Bias Fits

Description Usage Arguments Details Value Author(s) References See Also Examples

These utility functions convert data of format divided by amino acids into list of format divided by ORFs, or convert data to other formats.

  convert.reu13.df.to.list(reu13.df)
  convert.y.to.list(y)
  convert.n.to.list(n)

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

  codon.low2up(x)
  codon.up2low(x)

  dna.low2up(x)
  dna.up2low(x)

  convert.b.to.bVec(b)
  convert.bVec.to.b(bVec, aa.names, model = .CF.CT$model[1])

`reu13.df`	a list of `reu13.df` data frames divided by amino acids.
`y`	a list of `y` data frames divided by amino acids.
`n`	a list of `n` vectors divided by amino acids.
`seq.data`	a vector of `seq.data` format.
`x`	a codon or dna string, such "ACG", "acg", or "A", "a".
`b`	a `b` object.
`bVec`	a `bVec` object.
`aa.names`	a vector contains amino acid names for analysis.
`model`	model fitted.

convert.reu13.df.to.list(), convert.y.to.list(), and convert.n.to.list(): these utility functions take the inputs divided by amino acids and return the outputs divided by ORFs.

convert.y.scuo() converts y into scuo format.

convert.seq.data.to.string() converts seq.data into seq.string format.

codon.low2up() and codon.up2low() convert codon strings between lower or upper cases.

convert.bVec.to.b() and convert.b.to.bVec() convert objects b and bVec.

All functions return the corresponding formats.

Wei-Chen Chen wccsnow@gmail.com.

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

AllDataFormats, rearrange.n(), rearrange.reu13.df(), rearrange.y(), and read.seq().

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

reu13.list <- convert.reu13.df.to.list(ex.train$reu13.df)
y.list <- convert.y.to.list(ex.train$y)
n.list <- convert.n.to.list(ex.train$n)

scuo <- convert.y.to.scuo(ex.train$y)

seq.data <- read.seq(get.expath("seq_200.fasta"))
seq.string <- convert.seq.data.to.string(seq.data)

codon.low2up("acg")
codon.up2low("ACG")

dna.low2up(c("a", "c", "g"))
dna.up2low(c("A", "C", "G"))

## End(Not run)