IdClusters {DECIPHER} | R Documentation

## Cluster Sequences By Distance or Sequence

### Description

Groups the sequences into clusters of similarity or creates a tree from a set of sequences.

### Usage

    IdClusters(myDistMatrix = NULL,
               method = "UPGMA",
               cutoff = -Inf,
               showPlot = FALSE,
               type = "clusters",
               myXStringSet = NULL,
               model = MODELS,
               collapse = 0,
               reconstruct = FALSE,
               root = 0,
               processors = 1,
               verbose = TRUE)

### Arguments

`myDistMatrix` | A symmetric N x N distance matrix with the values of dissimilarity between N sequences, an object of class `'dist'`, or `NULL` if `method` is `"inexact"`.
`method` | An agglomeration method to be used. This should be (an abbreviation of) one of `"complete"`, `"single"`, `"UPGMA"`, `"WPGMA"`, `"NJ"`, `"ML"`, or `"inexact"`. (See details section below.)
`cutoff` | A vector with the maximum edge length separating the sequences in the same cluster. Multiple cutoffs may be provided in ascending or descending order. (See details section below.)
`showPlot` | Logical specifying whether or not to plot the resulting dendrogram. Not applicable if `method='inexact'`.
`type` | Character string indicating the type of output desired. This should be (an abbreviation of) one of `"clusters"`, `"dendrogram"`, or `"both"`. Not applicable if `method='inexact'`. (See value section below.)
`myXStringSet` | If `method` is `"ML"` or `reconstruct` is not `FALSE`, the `DNAStringSet` or `RNAStringSet` used in the creation of `myDistMatrix`. If `method` is `"inexact"`, the `DNAStringSet`, `RNAStringSet`, or `AAStringSet` to cluster.
`model` | One or more of the available `MODELS` of evolution. Only applicable if `method` is `"ML"` or `reconstruct` is not `FALSE`.
`collapse` | Numeric controlling which internal edges of the tree are removed by collapsing their nodes. If `collapse` is zero (the default) then nodes at the same height will be collapsed to a single node, resulting in a multifurcating tree. When `collapse` is greater than zero, nodes that are within `collapse` difference in height are made into a single node. A value of `collapse` less than zero will ensure that the `dendrogram` is purely bifurcating. Note that `collapse` has no effect on cluster numbers or `cutoff`.
`reconstruct` | Logical or numeric determining whether to perform ancestral state reconstruction. If `TRUE`, maximum likelihood character states are determined at internal nodes of the `dendrogram` and provided as the `"state"` attribute. A numeric value between zero and one (exclusive) can be provided, in which case that fraction of the likelihood for a state must be greater than the likelihood of all alternative states, otherwise a more ambiguous degeneracy code is used. Requires specification of a `DNAStringSet` or `RNAStringSet` via `myXStringSet`. Only applicable if `type` is `"dendrogram"` or `"both"`.
`root` | Integer specifying the index of the outgroup in `myDistMatrix`, or `0` (the default) to midpoint root the dendrogram.
`processors` | The number of processors to use, or `NULL` to automatically detect and use all available processors.
`verbose` | Logical indicating whether to display progress.

### Details

`IdClusters` groups the input sequences into clusters using a set of dissimilarities representing the distance between N sequences. For all `method`s except `"inexact"`, a phylogenetic tree is formed and each leaf (sequence) of the tree is assigned to a cluster based on its edge lengths to the other sequences. The available clustering methods are described as follows:

Ultrametric methods: The method `complete` assigns clusters using complete-linkage so that sequences in the same cluster are no more than `cutoff` distance apart. The method `single` assigns clusters using single-linkage so that sequences in the same cluster are within `cutoff` of at least one other sequence in the same cluster. `UPGMA` (the default) or `WPGMA` assign clusters using average-linkage which is a compromise between the sensitivity of complete-linkage clustering to outliers and the tendency of single-linkage clustering to connect distant relatives that do not appear to be closely related. `UPGMA` produces an unweighted tree, where each leaf contributes equally to the average edge lengths, whereas `WPGMA` produces a weighted result.

Additive methods: `NJ` uses the Neighbor-Joining method proposed by Saitou and Nei that does not assume lineages evolve at the same rate (the molecular clock hypothesis). The `NJ` method is typically the most phylogenetically accurate of the above distance-based methods. `ML` creates a neighbor-joining tree and then iteratively maximizes the likelihood of the tree given the aligned sequences (`myXStringSet`). This is accomplished through a combination of optimizing edge lengths with Brent's method and improving tree topology with nearest-neighbor interchanges (NNIs). When `method="ML"`, one or more `MODELS` of DNA evolution must be specified. Model parameters are iteratively optimized to maximize likelihood, except base frequencies which are empirically determined. If multiple `model`s are given, the best `model` is automatically chosen based on BIC calculated from the likelihood and the sample size (defined as the number of variable sites in the DNA sequence).

Sequence-only method: `inexact` uses a heuristic algorithm to directly assign sequences to clusters without a distance matrix. First the sequences are ordered by length and the longest sequence becomes the first cluster seed. If the second sequence is less than `cutoff` k-mer distance then it is added to the cluster, otherwise it becomes a new cluster representative. The remaining sequences are matched to cluster representatives in a similar fashion until all sequences belong to a cluster. In the majority of cases, this process results in clusters with members separated by less than `cutoff` distance.

For all `method`s, multiple cutoffs may be provided in sorted order. If the `cutoff`s are provided in descending order then clustering at each new value of `cutoff` is continued within the prior `cutoff`'s clusters. In this way clusters at lower values of `cutoff` are completely contained within their umbrella clusters at higher values of `cutoff`. This is useful for defining taxonomy, where groups need to be hierarchically nested. If multiple cutoffs are provided in ascending order then clustering at each level of `cutoff` is independent of the prior level. This may result in fewer high-level clusters for `NJ` and `ML` methods, but will have no impact on ultrametric methods unless `root` is greater than zero (i.e., outgroup rooted).

### Value

If `type` is `"clusters"` (the default), then a data.frame is returned with a column for each cutoff specified. This data.frame has dimensions N*M, where each one of N sequences is assigned to a cluster at the M-level of cutoff. The row.names of the data.frame correspond to the dimnames of `myDistMatrix`. If `type` is `"dendrogram"`, then an object of class `dendrogram` is returned that can be used for plotting. Leaves of the dendrogram are colored by cluster number, but the same color may be repeated for different clusters. Note that the cophenetic distance between leaves of the tree is equal to the sum of branch lengths separating the leaves. This is different than trees produced by `hclust` where leaves are merged at a height equal to their cophenetic distance. If `type` is `"both"` then a list is returned containing both the `"clusters"` and `"dendrogram"` outputs.

### Author(s)

Erik Wright eswright@pitt.edu

### References

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376.

Ghodsi, M., Liu, B., & Pop, M. (2011) DNACLUST. BMC Bioinformatics, 12(1), 271. doi:10.1186/1471-2105-12-271.

Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406-425.

### See Also

`Cophenetic`, `DistanceMatrix`, `Add2DB`, `MODELS`

### Examples

    # using the matrix from the original paper by Saitou and Nei
    m <- matrix(0,8,8) # only the lower triangle is used
    m[2:8,1] <- c(7, 8, 11, 13, 16, 13, 17)
    m[3:8,2] <- c(5, 8, 10, 13, 10, 14)
    m[4:8,3] <- c(5, 7, 10, 7, 11)
    m[5:8,4] <- c(8, 11, 8, 12)
    m[6:8,5] <- c(5, 6, 10)
    m[7:8,6] <- c(9, 13)
    m[8,7] <- c(8)

    # returns an object of class "dendrogram"
    tree <- IdClusters(m, cutoff=10, method="NJ", showPlot=TRUE, type="dendrogram")

    # example of specifying multiple cutoffs
    clusters <- IdClusters(m, type="clusters", cutoff=c(2,6,10,20)) # returns a data frame
    head(clusters)

    # example of creating a complete-linkage tree from an alignment
    fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER")
    dna <- readDNAStringSet(fas)
    dna # input alignment
    d <- DistanceMatrix(dna, type="dist") # returns an object of class 'dist'
    IdClusters(d, method="complete", cutoff=0.05, showPlot=TRUE, type="dendrogram")

    # example of 'inexact' clustering
    fas <- system.file("extdata", "50S_ribosomal_protein_L2.fas", package="DECIPHER")
    dna <- readDNAStringSet(fas)
    aa <- translate(dna)
    inexact <- IdClusters(myXStringSet=aa, method="inexact", cutoff=seq(0.7, 0.1, -0.1))
    head(inexact)
    apply(inexact, 2, max) # number of clusters per cutoff

[Package DECIPHER version 2.20.0 Index]