svdgram: Compute Phylogenetic Trees Using an n-Gram and SVD Approach

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

Computes phylogenetic trees using an n-gram and SVD approach.

Usage

svdgram(matrix, rank, species, SVS = TRUE)

Arguments

matrix	either a dataframe or a matrix where each row represents a property of a protein (for instance, the frequencies of tetrapeptides) and each column represents a different protein (or species).
rank	a numeric array providing the ranks that want to be used to approach the data matrix using SVD.
species	character array providing the species' names.
SVS	logical. When the matrix passed as argument correspond to the peptide-protein matrix and SVS is set to TRUE, then the function will compute a matrix where the columns are the Species Vector Sums. Alternatively, if the matrix passed as argument is already a matrix where the columns encode for species, SVS should be set to FALSE.

Details

When the matrix passed as argument is a matrix of peptide-protein, the function implement the method described by Stuart et al. 2002 (see references).

Value

An object of class multiPhylo containing a tree for each rank value required.

References

Stuart et al. Bioinformatics 2002; 18:100-108.

See Also

ngraMatrix()

Examples

a <- ngraMatrix(bovids[, 1:4], k = 2)[[2]][, -1]
species <- names(a)
svdgram(matrix = a, rank = 4, species = species, SVS = FALSE)

EnvNJ documentation built on Sept. 27, 2021, 5:07 p.m.