getEntropySignature: Infer Entropy Signature

In MetaEntropy: Functional Shannon Entropy for Virome Mutational Analysis

Infer Entropy Signature

Description

Calculates genome-wide Shannon entropies from SNV data.

Usage

getEntropySignature(
  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",
  categories = "robust",
  genome = mn908947.3
)

Arguments

polymorphisms	A data frame. Please see Details and Examples.
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.
categories	Whether a class per amino acid should be used ("sensitive") or they should be grouped into aliphatic, aromatic, polar, positively charged, negatively charged, and special ("robust") (Mirny and Shakhnovich, 1999).
genome	A list providing CDS data and length of the reference genome.

Details

You provide a data frame with SNVs information including reference and alternative aminoacids, their frequencies, and corresponding positions relative to a reference sequence. This type of data can be generated by numerous programs and pipelines. The objective is to assess the biological impact of nonsynonymous variation within a viral population, such as an environmental sample (e.g. wastewater) or a single infection (aka quasisepecies). Entropy is calculated within the metagenome and is therefore independent of the reference sequence. Some mutations may be part of a same codon. This is to be indicated in the linkage column, providing a downstream linked position, or the closest upstream position if there are no downstream positions that are part of the same codon. For example, in the wWater dataset, mutations T22673C and C22674T are linked to each other and affect codon 371 of the S gene:

	wave	position	linkage	ref	alt	protein	...
...
105	third	22599	NA	G	A	S	...
106	third	22673	22674	T	C	S	...
107	third	22674	22673	C	T	S	...
108	third	22679	NA	T	C	S	...
...

The genome parameter is a list that provides data on the topology of protein-coding regions in the genome and its length, used internally primarily for graphical and summary purposes. The package provides an example (mn908947.3) of how this information is to be organized.

Value

An object of class entropyProfile. It contains a tidy, summarized version of the SNV table, a data frame with information on genome-wide entropy, a data frame with information on each CDS and corresponding mutations observed in the virome, and a list with CDS data and length of the reference genome used in variant calling.

References

Mirny and Shakhnovich, 1999. J Mol Biol 291:177-196. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1006/jmbi.1999.2911")}.

Shannon, 1948. Bell System Technical Journal, 27:379-423. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/j.1538-7305.1948.tb01338.x")}.

Examples

# Entropy across the genome in ancestral lineages
ancestral <- getEntropySignature(wWater[wWater$wave == "first", ], categories = "sensitive")

# Inspect profile
plot(ancestral, chartType = "entroScan")

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