entropyProfile: Create (empty) object of class "entropyProfile"

In MetaEntropy: Functional Shannon Entropy for Virome Mutational Analysis

Create (empty) object of class "entropyProfile"

Description

This function is intended primarily for internal use by getEntropySignature.

Usage

entropyProfile(
  polymorphisms,
  position = "position",
  linkage = "linkage",
  ref = "ref",
  alt = "alt",
  protein = "protein",
  aa_position = "aa_position",
  ref_aa = "ref_aa",
  alt_aa = "alt_aa",
  alt_aa_freq = "alt_aa_freq",
  entropies = NA_real_,
  genome = mn908947.3
)

Arguments

polymorphisms	A data frame. Please see Details and Examples in documentation for getEntropySignature.
position	Name of the polymorphisms's column that indicates SNV locations in the genome.
linkage	Information on linked positions.
ref	Column name with reference bases.
alt	Column name with the alternative bases observed in the metagenome.
protein	Name of the column carrying protein names.
aa_position	Name of the column that indicates the protein positions of the mutated amino acids.
ref_aa	Name of the column that carries the reference amino acids.
alt_aa	Name of the column carrying alternative amino acids observed in the metagenome.
alt_aa_freq	Name of the column giving the frequencies of alternative amino acids in the metagenome.
entropies	NA_REAL_ (double numeric/real vector to hold entropy values).
genome	A list providing CDS data and length of the reference genome.

Details

The documentation for getEntropySignature details the type of input needed to create a profile. entropyProfile uses the same parameters as getEntropySignature, with the exception of categories and entropies.

Value

An (empty) object of class entropyProfile.

See Also

getEntropySignature.

MetaEntropy documentation built on March 3, 2026, 5:08 p.m.