TASSO: Fit the Tree-guided Automatic Sub-composition Selection...
In liudoubletian/phyloMDA: An R package for phylogeny-aware microbiome data analysis
TASSO R Documentation
Fit the Tree-guided Automatic Sub-composition Selection Operator (TASSO) model.
Description
Fit the Tree-guided Automatic Sub-composition Selection Operator (TASSO) model.
Usage
TASSO(y, X, tree = NULL)
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
when tree=NULL, it reduces to constrained lasso.
Value
Returns a genlasso object.
References
Wang, T., Zhao, H.: Structured subcomposition selection in regression and its application to microbiome data analysis. The Annals of Applied Statistics 11(2), 771–791 (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$bmi
fit <- TASSO(y, X, tree)
IC <- ICgenlasso(fit, IC='AIC')
IC <- ICgenlasso(fit, IC='BIC')
liudoubletian/phyloMDA documentation built on April 28, 2022, 6:51 p.m.
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| TASSO | R Documentation |
Fit the Tree-guided Automatic Sub-composition Selection Operator (TASSO) model.
Description
Fit the Tree-guided Automatic Sub-composition Selection Operator (TASSO) model.
Usage
TASSO(y, X, tree = NULL)
Arguments
y |
the univariate response. |
X |
a data frame or matrix containing the compositional data. Rows of the matrix represent observations and columns are the taxa. |
tree |
when tree=NULL, it reduces to constrained lasso. |
Value
Returns a genlasso object.
References
Wang, T., Zhao, H.: Structured subcomposition selection in regression and its application to microbiome data analysis. The Annals of Applied Statistics 11(2), 771–791 (2017).
Examples
library(phyloseq) otu.tab <- t(otu_table(combo.phyloseq.obj)) X <- eBay_comps(otu.tab, prior = "Dirichlet") tree <- phy_tree(combo.phyloseq.obj) metadata <- sample_data(combo.phyloseq.obj) y <- metadata$bmi fit <- TASSO(y, X, tree) IC <- ICgenlasso(fit, IC='AIC') IC <- ICgenlasso(fit, IC='BIC')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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