bClust: Clustering sequences based on pairwise distances
In micropan: Microbial Pan-Genome Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Sequences are clustered by hierarchical clustering based on a set of pariwise distances. The distances must take values between 0.0 and 1.0, and all pairs not listed are assumed to have distance 1.0.

1	bClust(dist.tbl, linkage = "complete", threshold = 0.75, verbose = TRUE)

`dist.tbl`	A `tibble` with pairwise distances.
`linkage`	A text indicating what type of clustering to perform, either complete (default), average or single.
`threshold`	Specifies the maximum size of a cluster. Must be a distance, i.e. a number between 0.0 and 1.0.
`verbose`	Logical, turns on/off text output during computations.

Computing clusters (gene families) is an essential step in many comparative studies. bClust will assign sequences into gene families by a hierarchical clustering approach. Since the number of sequences may be huge, a full all-against-all distance matrix will be impossible to handle in memory. However, most sequence pairs will have an ‘infinite’ distance between them, and only the pairs with a finite (smallish) distance need to be considered.

This function takes as input the distances in dist.tbl where only the relevant distances are listed. The columns Query and Hit contain tags identifying pairs of sequences. The column Distance contains the distances, always a number from 0.0 to 1.0. Typically, this is the output from bDist. All pairs of sequences not listed are assumed to have distance 1.0, which is considered the ‘infinite’ distance. All sequences must be listed at least once in ceither column Query or Hit of the dist.tbl. This should pose no problem, since all sequences must have distance 0.0 to themselves, and should be listed with this distance once (Query and Hit containing the same tag).

The linkage defines the type of clusters produced. The threshold indicates the size of the clusters. A single linkage clustering means all members of a cluster have at least one other member of the same cluster within distance threshold from itself. An average linkage means all members of a cluster are within the distance threshold from the center of the cluster. A complete linkage means all members of a cluster are no more than the distance threshold away from any other member of the same cluster.

Typically, single linkage produces big clusters where members may differ a lot, since they are only required to be close to something, which is close to something,...,which is close to some other member. On the other extreme, complete linkage will produce small and tight clusters, since all must be similar to all. The average linkage is between, but closer to complete linkage. If you want the threshold to specify directly the maximum distance tolerated between two members of the same gene family, you must use complete linkage. The single linkage is the fastest alternative to compute. Using the default setting of single linkage and maximum threshold (1.0) will produce the largest and fewest clusters possible.

The function returns a vector of integers, indicating the cluster membership of every unique sequence from the Query or Hit columns of the input dist.tbl. The name of each element indicates the sequence. The numerical values have no meaning as such, they are simply categorical indicators of cluster membership.

Lars Snipen and Kristian Hovde Liland.

bDist, hclust, dClust, isOrtholog.

# Loading example BLAST distances
data(xmpl.bdist)

# Clustering with default settings
clst <- bClust(xmpl.bdist)
# Other settings, and verbose
clst <- bClust(xmpl.bdist, linkage = "average", threshold = 0.5, verbose = TRUE)