SNP-distance sequence clustering

Formula: SNP-distance + linkage threshold

Usage

Cluseq(sequences, snp_threshold = 5)

Arguments

sequences: Aligned sequences of equal length.
snp_threshold: Maximum SNP distance for a link.

Value

List with estimate, z, counts, n_clusters, distances, max_distance, n, method.

Details

Pairwise SNP distances are computed on the aligned sequences and isolates are joined into a cluster whenever ANY pair is within the threshold – single linkage, which is what makes the result a transitive closure rather than a set of cliques. A threshold of zero leaves every distinct sequence on its own; a threshold at least as large as the diameter collapses everything into one cluster.

References

Croucher et al. (2015), Nucleic Acids Research 43(3):e15.

Examples

V <- c(1, 2, 3, 4, 5, 6, 7, 8)
Cluseq(V)
#> $estimate
#> [1] 1
#> 
#> $z
#> [1] 0 0 0 0 0 0 0 0
#> 
#> $counts
#> [1] 8
#> 
#> $n_clusters
#> [1] 1
#> 
#> $distances
#>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,]    0    1    1    1    1    1    1    1
#> [2,]    1    0    1    1    1    1    1    1
#> [3,]    1    1    0    1    1    1    1    1
#> [4,]    1    1    1    0    1    1    1    1
#> [5,]    1    1    1    1    0    1    1    1
#> [6,]    1    1    1    1    1    0    1    1
#> [7,]    1    1    1    1    1    1    0    1
#> [8,]    1    1    1    1    1    1    1    0
#> 
#> $max_distance
#> [1] 1
#> 
#> $n
#> [1] 8
#> 
#> $method
#> [1] "SNP-distance single-linkage sequence clustering"
#> 
#> attr(,"class")
#> [1] "morie_rich_result" "list"