TreeFusedlasso: Fit the tree-guided fused lasso model.

In liudoubletian/phyloMDA: An R package for phylogeny-aware microbiome data analysis

Fit the tree-guided fused lasso model.

Description

Fit the tree-guided fused lasso model.

Usage

TreeFusedlasso(y, X, tree, type = 1)

Arguments

y	the univariate response.
X	a data frame or matrix containing the compositional data. Rows of the matrix represent observations and columns are the taxa.
tree	the phylogenetic tree.
type	two different penalty construct methods : 1 or 2.

Value

Returns a genlasso object.

References

Wang, T., Zhao, H.: Constructing predictive microbial signatures at multiple taxonomic levels. Journal of the American Statistical Association 112(519), 1022–1031 (2017).

Examples

library(phyloseq)
otu.tab <- t(otu_table(combo.phyloseq.obj))
X <- eBay_comps(otu.tab, prior = "Dirichlet")
tree <- phy_tree(combo.phyloseq.obj)
metadata <- sample_data(combo.phyloseq.obj)
y <- metadata$bmi
fit <- TreeFusedlasso(y, X, tree)
IC <- ICgenlasso(fit, IC='AIC')
IC <- ICgenlasso(fit, IC='BIC')

liudoubletian/phyloMDA documentation built on April 28, 2022, 6:51 p.m.