concat_conserved_kmer {vDiveR}

k-mer sequences concatenation

Description

This function concatenates completely (index incidence = 100 index incidence < 100 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