"Refining and extending generalized multivariate linear models
for meta-omic association discovery"
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Documentation for package ‘maaslin3’ version 1.0.0
Help Pages
| maaslin3 | MaAsLin 3: A multivariable statistical framework for finding abundance and prevalence associations between metadata and high-dimensional microbial multi-omics data. |
| maaslin_check_arguments | Check parameter arguments to ensure a successful MaAsLin 3 run. |
| maaslin_check_formula | Check a MaAsLin 3 formula to ensure a proper MaAsLin 3 run. |
| maaslin_compute_formula | Compute a formula for a MaAsLin 3 run based on the specified effects. |
| maaslin_contrast_test | Perform a contrast from a fit MaAsLin 3 model. |
| maaslin_filter | Filter abundance data before MaAsLin 3 model fitting. |
| maaslin_fit | Fit MaAsLin 3 models. |
| maaslin_log_arguments | Log MaAsLin 3 parameters. |
| maaslin_normalize | Normalize abundance data for MaAsLin 3 model fitting. |
| maaslin_plot_results | Plot the results from a MaAsLin 3 run. |
| maaslin_plot_results_from_output | Plot the results from a MaAsLin 3 run. |
| maaslin_process_metadata | Process metadata before MaAsLin 3 model fitting. |
| maaslin_read_data | Read in the abundance data and metadata. |
| maaslin_reorder_data | Reorder the abundance data and metadata. |
| maaslin_transform | Transform abundance data for MaAsLin 3 modeling. |
| maaslin_write_results | Write the results from a MaAsLin 3 run. |
| maaslin_write_results_lefse_format | Write the results from a MaAsLin 3 run in LEfSe format. |
| preprocess_dna_mtx | Pre-process the DNA covariates for metatranscriptomics |
| preprocess_taxa_mtx | Pre-process the taxa covariates for metatranscriptomics |