BCCluster: Barcode clustering

In eberlejonas/TaxCI: Calculate the Consistency Index and the Retention Index for taxonomic data

Description

Barcode clustering using localMinima{spider}. The first local minimum is used for clustering.

Usage

BCCluster(data, x, method="spider", sp.col="sp", distmodel="K80", pairwise.deletion=FALSE, fix.threshold=NA)

## S3 method for class 'BCCluster'\cr
print.BCCluster(x, ...)

Arguments

data	If method is "spider" (the default): a matrix or a list containing the DNA sequences; this must be of class "DNAbin" (use as.DNAbin is they are stored as character) (Copied from dist.dna). If method is "external": a data.frame with two colums, the first containing specimen labels as in the taxonomic information and the second with integers describing cluster affiliation.
x	A table with taxonomic information (must contain a column with species names which is specified with sp.col). rownames(x) must exactly match rownames(alignment). For S3 method BCCluster an object of class BCCluster.
method	Either "spider" to use the package spider to infer clusters or "external" if the user supplies a clustering table (see 'data').
sp.col	The name or number of the column of x that contains species names
distmodel	Copied from dist.dna: a character string specifying the evolutionary model to be used; must be one of "raw", "N", "TS", "TV", "JC69", "K80" (the default), "F81", "K81", "F84", "BH87", "T92", "TN93", "GG95", "logdet", "paralin", "indel", or "indelblock".
pairwise.deletion	passed to dist.dna: a logical indicating whether to delete the sites with missing data in a pairwise way. The default is to delete the sites with at least one missing data for all sequences (ignored if model = "indel" or "indelblock").
fix.threshold	If NA, threshold is estimated my tclust. Else distance cutoff for clustering. E.g. 0.01 (1%).
...	Unused.

Details

Finds distance based barcode-clusters using spider-functions. Some summarizing and preparing is done for Taxonomic Consistency analyses.

Value

A list with the following elements:

clusters	A list of clusters, each containing the respective specimen names.
sp.in.clusters	A list of clusters, each containing the names of species that are in the respective cluster.
homogen	A vector containing the indices of homogeneous clusters. (Only one species contained.)
heterogen	A vector containing the indices of heterogeneous clusters. (More than one species contained.)
no.clusters	The number of clusters inferred.
no.homogeneous	The number of homogeneous clusters.
no.heterogeneous	The number of homogeneous clusters.
sp.col	User-set column of x containing species information.
threshold	The local minimum threshold that was used or the fixed threshold.

Author(s)

Jonas Eberle

See Also

See TaxCI for example.

Related: localMinima, tclust, read.dna, dist.dna

eberlejonas/TaxCI documentation built on July 20, 2021, 9:46 a.m.