apply.test: Apply different tests to the simulated data

In zellerlab/SIMBA: Simulation of Microbiome Data with Biological Accuracy

Apply different tests to the simulated data

Description

This function applies one of the implemented differential abundance testing methods to a dataset within the simulation

Usage

apply.test(sim.location, group, type='default',
subset=NA_real_, norm='pass',
test='wilcoxon', conf=NULL, ...)

Arguments

sim.location	file name for the .h5 file containing the simulations
group	character, name of the group within the .h5 file containing the simulated features
type	character, name of the index group within the .h5 file containing the testing or bootstrapping indices Can be either "default", "biomarker", "confounder", or "random"
subset	vector, subset size(s) to be tested
norm	character, normalization method to be applied before testing
test	character, differential abundance testing method
conf	character, name of the confounder metadata column
...	additional parameters (for experts)

Details

todo

Value

This function returns a list of P-values matrices

zellerlab/SIMBA documentation built on June 2, 2025, 6:25 a.m.