odmix {odseq}R Documentation

Gaussian mixture modelling of distances in a multiple sequence alignment.

Description

This function performs clustering of biological sequences via fitting a Gaussian mixture model of the distances defined by the odseq algorithm

Usage

odmix(msa_object, distance_metric, groups)

Arguments

msa_object

An object of formal class MsaAAMultipleAlignment, as provided by the msa package.

distance_metric

A string indicating the type of distance metric to be computed. Either 'linear' and 'affine' is supported at the moment.

groups

Number of groups to fit in the mixture model. If a numeric vector of size n, n models will be fitted and a list of BIC values will be given to choose a single model.

Value

A list containing the following items:

prob

A numeric matrix of size n x groups where the probability of belonging to a group is provided for each sequence.

class

The class assigned according to prob. Returns a numeric vector.

BIC

BIC values for the models proposed in groups

Author(s)

José Jiménez <jose@jimenezluna.com>

See Also

odseq_unaligned odseq

Examples

library(msa)
data(seqs)
al <- msa(seqs)
odmix(al, distance_metric = "affine", groups = 2)

[Package odseq version 1.21.0 Index]