EnvNJ (version 0.1.3)

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

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.

Value

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

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).

References

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

See Also

ngraMatrix()

Examples

# NOT RUN {
a <- ngraMatrix(bovids[, 1:4], k = 2)[[2]][, -1]
species <- names(a)
svdgram(matrix = a, rank = 4, species = species, SVS = FALSE)
# }