sccoda.model.other_models.ANCOMBCModel.fit_model

ANCOMBCModel.fit_model(method='fdr', lib_cut=0, r_home='', r_path='', alpha=0.05, zero_cut=0.9)

Fits ANCOM with bias correction model.

Parameters

method : strstr (default: 'fdr')

method that is used to calculate p-values

lib_cut : intint (default: 0)

threshold to filter out classes

r_home : strstr (default: '')

path to R installation on your machine, e.g. “C:/Program Files/R/R-4.0.3”

r_path : strstr (default: '')

path to R executable on your machine, e.g. “C:/Program Files/R/R-4.0.3/bin/x64”

alpha : floatfloat (default: 0.05)

Nominal FDR value

zero_cut : floatfloat (default: 0.9)

Prevalence cutoff for cell types (cell types with higher percentage of zero entries are dropped)