phylo2sbp: Create Sequential Binary Partition from Phylogenetic Tree

In philr: Phylogenetic partitioning based ILR transform for metagenomics data

Description

This function converts a binary phylogenetic tree to sequential binary parition to be used to then build an ILR basis for compositional metagenomic data.

Usage

phylo2sbp(tr)

Arguments

tr	a phylo tree object with n leaves

Details

The choice of orientation for a balance (i.e., which of the two descendant clades of an internal node is in the numerator or denominator of the log-ratio) is given by the default of the function phangorn::Children and that choise is used consistently throughout the philr package.

Value

a n by n-1 matrix of the sequential binary partition sign matrix

Author(s)

Justin Silverman

References

Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

See Also

philr

Examples

tr <- named_rtree(5)
phylo2sbp(tr)

Example output

   n1 n2 n3 n4
t2  1  1  1  0
t3  1  1 -1  0
t5  1 -1  0  0
t4 -1  0  0  1
t1 -1  0  0 -1

philr documentation built on Nov. 8, 2020, 5:38 p.m.