## ----eval=FALSE--------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Maaslin2") ## ----------------------------------------------------------------------------- library(Maaslin2) input_data <- system.file( 'extdata','HMP2_taxonomy.tsv', package="Maaslin2") input_metadata <-system.file( 'extdata','HMP2_metadata.tsv', package="Maaslin2") fit_data <- Maaslin2( input_data, input_metadata, 'demo_output', fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'), random_effects = c('site', 'subject'), reference = "diagnosis,nonIBD", standardize = FALSE) ## ----------------------------------------------------------------------------- sessionInfo()