Data Formats {cubfits} | R Documentation

## Data Formats

### Description

Data formats used in cubfits.

### Format

All are in simple formats as S3 default lists or data frames.

### Details

- Format `b`:
  A named list `A` contains amino acids. Each element of the list `A[[i]]` is a list of elements `coefficients` (coefficients of log(mu) and Delta.t), `coef.mat` (matrix format of `coefficients`), and `R` (covariance matrix of `coefficients`). Note that `coefficients` and `R` are typically as in the output of `vglm()` of VGAM package. Also, `coef.mat` and `R` may miss in some cases.
  e.g. `A[[i]]$coef.mat` is the regression beta matrix of `i`-th amino acid.

- Format `bVec`:
  A vector simply contains all coefficients of a `b` object `A`. Note that this is probably only used inside MCMC or the output of `vglm()` of VGAM package.
  e.g. `do.call("c", lapply(A, function(x) x$coefficients))`.

- Format `n`:
  A named list `A` contains amino acids. Each element of the list `A[[i]]` is a vector containing total codon counts.
  e.g. `A[[i]][j]` is for `j`-th ORF of `i`-th amino acid `names(A)[i]`.

- Format `n.list`:
  A named list `A` contains ORFs. Each element of the list `A[[i]]` is a named list of amino acid containing total count.
  e.g. `A[[i]][[j]]` contains total count of `j`-th amino acid in `i`-th ORF.

- Format `phi.df`:
  A data frame `A` contains two columns `ORF` and `phi.value`.
  e.g. `A[i,]` is for `i`-th ORF.

- Format `reu13.df`:
  A named list `A` contains amino acids. Each element is a data frame summarizing ORF and expression. The data frame has four to five columns including `ORF`, `phi` (expression), `Pos` (amino acid position), `Codon` (synonymous codon), and `Codon.id` (synonymous codon id, for computing only). Note that `Codon.id` may miss in some cases.
  e.g. `A[[i]][17,]` is the 17-th recode of `i`-th amino acid.

- Format `reu13.list`:
  A named list `A` contains ORFs. Each element is a named list `A[[i]]` contains amino acids. Each element of nested list `A[[i]][[j]]` is a position vector of synonymous codon.
  e.g. `A[[i]][[j]][k]` is the `k`-th synonymous codon position of `j`-th amino acid in the `i`-th ORF.

- Format `scuo`:
  A data frame of 8 named columns includes `AA` (amino acid), `ORF`, `C1`, ..., `C6` where `C*`'s are for codon counts.

- Format `seq.string`:
  Default outputs of `read.fasta()` of seqinr package. A named list `A` contains ORFs. Each element of the list is a long string of a ORF.
  e.g. `A[[i]][1]` or `A[[i]]` is the sequence of `i`-th ORF.

- Format `seq.data`:
  Converted from `seq.string` format. A named list `A` contains ORFs. Each element of the list `A[[i]]` is a string vector. Each element of the vector is a codon string.
  e.g. `A[[i]][j]` is `i`-th ORF and `j`-th codon.

- Format `phi.Obs`:
  A named vector `A` of observed expression values and possibly with measurement errors.
  e.g. `A[i]` is the observed phi value of `i`-th ORF.

- Format `y`:
  A named list `A` contains amino acids. Each element of the list `A[[i]]` is a matrix where ORFs are in row and synonymous codons are in column. The element of the matrix contains codon counts.
  e.g. `A[[i]][j, k]` is the count for `i`-th amino acid, `j`-th ORF, and `k`-th synonymous codon.

- Format `y.list`:
  A named list `A` contains ORFs. Each element of the list `A[[i]]` is a named list `A[[i]][[j]]` contains amino acids. The element of amino acids list is a codon count vector.
  e.g. `A[[i]][[j]][k]` is the count for `i`-th ORF, `j`-th amino acid, and `k`-th synonymous codon.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com.

### References

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

[Package cubfits version 0.1-3 Index]