codonFreq-class: S4 class for storing relative codon frequencies in...

In adamd3/codondiffR: Codon usage comparisons across taxa

S4 class for storing relative codon frequencies in user-supplied sequences.

Description

S4 class for storing relative codon frequencies in user-supplied sequences.

Usage

codonFreq(object)

getFreqs(object)

nseq(object)

seqID(object)

seqlen(object)

codonPlot(
  object,
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  groups = NULL,
  ptype = "boxplot",
  order = "median",
  colour = 1,
  suppress_x_txt = FALSE,
  suppress_y_title = FALSE,
  label = NULL,
  highlight = NULL,
  save = FALSE
)

normalise(object)

## S4 method for signature 'codonFreq'
getFreqs(object)

## S4 method for signature 'codonFreq'
nseq(object)

## S4 method for signature 'codonFreq'
seqID(object)

## S4 method for signature 'codonFreq'
seqlen(object)

Arguments

object

An object of class codonFreq.

Value

Matrix, frequencies of codons in the codonFreq object. Codons are in columns and input sequences are in rows.

Numeric, the number of sequences in the codonFreq object.

Character, the identifiers of sequences in the codonFreq object.

Numeric, lengths of sequences (in codons).

Methods (by generic)

• getFreqs: Returns the relative frequencies of codons per sequence in a codonFreq object.

• nseq: Returns the number of sequences in a codonFreq object.

• seqID: Returns the sequence identifiers in a codonFreq object.

• seqlen: Returns the lengths of sequences (in codons) in a codonFreq object.

Slots

seqID

Character vector of sequence identifiers, derived from Fasta identifier lines.

freq

Matrix containing the relative frequencies of codons; each sequence is a row and each codon is a column.

ncod

Numeric vector of sequence lengths (in codons).

adamd3/codondiffR documentation built on Sept. 3, 2022, 2:26 a.m.