create.data.simulation: Simulate metagenomic features

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

Simulate metagenomic features

Description

This function uses a feature and metadata table as well as specific parameters to create simulated metagenomic samples and stores those in the indicated .h5 file

Usage

create.data.simulation(feat, meta, sim.location,
sim.method='resampling',
sim.type="cross-section",
filt.params=list(prev.cutoff=0.05, ab.cutoff=1e-04, log.n0=1e-05),
sim.params=list(class.balance=0.5, prop.markers=0.1, conf = 'None',
ab.scale=c(1.0, 1.25, 1.5, 2.0, 5.0, 10.0, 20.0),
prev.scale=c(0.0, 0.1, 0.2, 0.3),
repeats=100, feature.type='all'))

Arguments

feat	feature matrix, can be either a single matrix or a list of matrices from different studies
meta	metadata about samples in the features matrix, should be a dataframe or a list of dataframes
sim.location	filename for an .h5 file which will store the simulations, original data, and simulation parameters
sim.method	methodology to create the simulations. Can either be a string describing a pre-implemented method or a user-specified function (see Details below). Defaults to "resampling"
sim.type	character, can be either "cross-section" or "time-course", defaults to 'cross-section'
filt.params	list of parameters for data filtering, defaults to filt.params=list(prev.cutoff=0.05, ab.cutoff=1e-04, log.n0=1e-05), see Details below
sim.params	list of parameters which are given to the sim.method function, see Details

Details

This functions TODO

Filtering Pre-implemented Simulations Simulations h5-File Organisation

Value

Does not return anything but instead creates an h5 file containing simulated samples

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