showMutations: Summarize mutations

In MetaEntropy: Functional Shannon Entropy for Virome Mutational Analysis

Summarize mutations

Description

Displays SNVs, and corresponding protein mutations, at specific genomic positions.

Usage

showMutations(profile, positions)

Arguments

profile	An object of class entropyProfile.
positions	A vector with genome positions relative to the reference genome.

Details

The user provides a list of genome positions and the function prints the mutations associated with them. The output format is "ref_res###alt_res / protein:ref_res###alt_res", where ref_res is the residue (eiter nucleotide or aminoacid) in the reference strain, alt_res is the alternative residue in the metagenome, "###" is the position (either nucleotide or aminoacid) where the mutation was observed, and "protein" is the name of the affected protein.

Value

An object of class c("tidyMutations", "data.frame"), containing summary information about user-supplied genomic positions. This information includes the mutations themselves relative to the reference genome, their positions within it, and the corresponding abundances in the virome. Intended to be displayed by print.tidyMutations.

See Also

getEntropySignature.

Examples

# High entropy at the RBD in Omicron lineages
omicron <- getEntropySignature(wWater[wWater$wave == "third", ])
plot(omicron, chartType="stripchart")

# Identify the high-entropy positions
omicron$Entropy$position[ omicron$Entropy$entropy > 0.3 ]
#[1] 22882 22898 22917 23013 23040 23048 23055 23063

# Get a descriptive table
showMutations(omicron, c(22882, 22898, 22917, 23013, 23040, 23048, 23055, 23063))

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