MiAF: Microbiome Adaptive Fisher Test

In songbiostat/MiAF: Microbiome Adaptive Fisher Test

Description

Microbiome Adaptive Fisher Test

Usage

MiAF(Y, X, tree, cov = NULL, model = c("gaussian", "binomial"), n.perm, seed)

Arguments

Y	A numeric vector for continuous or binary responses.
X	A matrix of the OTU table. Row - samples, column - OTUs.
tree	A rooted phylogenetic tree of R class "phylo".
cov	A data frame/matrix for covariate adjustment. Row - samples, column - covariates.
model	"gaussian" is for the linear regression model (continuous); "binomial" is for the logistic regression model (binary).
n.perm	The number of permutations.
seed	set seed.

Value

A list containing the following elements:

UniFrac	Unweighted UniFrac-like test p-value.
wUniFrac	Weighted UniFrac-like test p-value.
UniFrac5	Generalized UniFrac-like test p-value.
tip.abun	Leaf-nodes-only test p-value.
com	The p-value of MiAF test that combines p-values of the above four tests.
select	A list of selected associated taxa. lower: under-presented taxa based on lower-tail p-values. upper: over-presented taxa based on upper-tail p-values.

songbiostat/MiAF documentation built on Feb. 18, 2022, 10:29 p.m.