Maaslin2_wrapper: Wrapper function for Maaslin2

In biobakery/MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

Wrapper function for Maaslin2

Description

Wrapper function for Maaslin2

Usage

Maaslin2_wrapper(feature_abd, data, exposure, covariates = NULL,
  covariates_random = NULL, output = tempdir(),
  normalization = "TSS", transform = "AST", analysis_method = "LM")

Arguments

feature_abd	feature*sample matrix of feature abundance.
data	data frame of metadata.
exposure	name of exposure variable.
covariates	name of covariates.
covariates_random	name of random covariates.
output	directory for Maaslin2.
normalization	normalization parameter for Maaslin2.
transform	transformation parameter for Maaslin2.
analysis_method	analysis method parameter for Maaslin2.

Value

a data frame recording per-feature coefficients, p-values, etc. from running Maaslin2.

biobakery/MMUPHin documentation built on March 30, 2024, 4:50 a.m.