fine_cluster_seqs {CellaRepertorium} | R Documentation

## Calculate distances and perform hierarchical clustering on a set of sequences

### Description

The distances between AA sequences is defined to be 1-score/max(score) times the median length of the input sequences. The distances between nucleotide sequences is defined to be edit_distance/max(edit_distance) times the median length of input sequences.

### Usage

    fine_cluster_seqs(
      seqs,
      type = "AA",
      big_memory_brute = FALSE,
      method = "levenshtein",
      substitution_matrix = "BLOSUM100",
      cluster_fun = "none",
      cluster_method = "complete"
    )

### Arguments

`seqs` | character vector, DNAStringSet or AAStringSet
`type` | character either `AA` or `DNA` specifying type of `seqs`
`big_memory_brute` | attempt to cluster more than 4000 sequences? Clustering is quadratic, so this will take a long time and might exhaust memory
`method` | one of 'substitutionMatrix' or 'levenshtein'
`substitution_matrix` | a character vector naming a substitution matrix available in Biostrings, or a substitution matrix itself
`cluster_fun` | `character`, one of "hclust" or "none", determining if distance matrices should also be clustered with `hclust`
`cluster_method` | character passed to `hclust`

### Value

`list`

### See Also

`hclust()`, `Biostrings::stringDist()`

### Examples

    fasta_path = system.file('extdata', 'demo.fasta', package='CellaRepertorium')
    aaseq = Biostrings::readAAStringSet(fasta_path)[1:100]
    cls = fine_cluster_seqs(aaseq, cluster_fun = 'hclust')
    plot(cls$cluster)

[Package CellaRepertorium version 1.2.0 Index]