concat_conserved_kmer: k-mer sequences concatenation

In vDiveR: Visualization of Viral Protein Sequence Diversity Dynamics

k-mer sequences concatenation

Description

This function concatenates completely ( index incidence = 100% ) only or both both the completely and highly ( 90% <= index incidence < 100% ) conserved k-mer positions that overlapped at least one k-mer position or are adjacent to each other and generate the CCS/HCS sequence in either CSV or FASTA format

Usage

concat_conserved_kmer(
  data,
  conservation_level = "HCS",
  kmer = 9,
  threshold_pct = NULL
)

Arguments

data	DiMA JSON converted csv file data
conservation_level	CCS (completely conserved) / HCS (highly conserved)
kmer	size of the k-mer window
threshold_pct	manually set threshold of index.incidence for HCS

Value

A list wit csv and fasta dataframes

Examples

csv<-concat_conserved_kmer(proteins_1host)$csv
csv_2hosts<-concat_conserved_kmer(protein_2hosts, conservation_level = "CCS")$csv
fasta <- concat_conserved_kmer(protein_2hosts, conservation_level = "HCS")$fasta

vDiveR documentation built on May 11, 2026, 9:07 a.m.