VIProDesign (version 0.1.0)

phyl_tree_cluster_dbscan: Perform DBSCAN Clustering on a Phylogenetic Tree

Description

This function applies the DBSCAN clustering algorithm on a set of protein sequences to identify clusters and remove outliers based on a distance cutoff.

Usage

phyl_tree_cluster_dbscan(input_obj, cutoff, nmin)

Value

This function returns a `AAStringSet` object containing protein sequences with outliers removed.

Arguments

input_obj

A `AAStringSet` object containing protein sequences.

cutoff

A numeric value specifying the distance cutoff for clustering.

nmin

An integer specifying the minimum number of points required to form a cluster (DBSCAN parameter).

Details

The function uses the DBSCAN algorithm to cluster sequences based on their phylogenetic distances. Sequences identified as outliers are excluded from the final output.

Examples

# Example usage:
library(Biostrings)

# Create an AAStringSet object with the sequences
seqs <- AAStringSet(c(
  seq1 = "MKTIIALSYIFCLVFADYKDDDDK",
  seq2 = "MKTIIALSYIFCLVFADYKDLLKDDDD",
  seq3 = "MKTIIALSYIFCLVFADEELYKDDDD",
  seq4 = "MKTIEIALSYIFCLVFADYKDDDD",
  seq5 = "MKTIIKLAAASYIFCLVFADYKDDDD",
  seq6 = "MKTIIALSKIPFCLVFADYKDDDD",
  seq7 = "MKTIIALSYIFiQEERTCLVFADYKDDDD"
))

# Perform DBSCAN clustering and remove outliers
no_outliers <- phyl_tree_cluster_dbscan(seqs, cutoff = 0.5, nmin = 5)