| Class | Description |
|---|---|
| AddMetadataToTaxaTables |
This BioModule is used to add metadata columns to the OTU abundance tables.
|
| BuildTaxaTables |
Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level.
|
| LogTransformTaxaTables |
This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.
|
| NormalizeTaxaTables |
This utility is used to normalize and/or log-transform the raw OTU counts using the formulas:
Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1
Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ]
The code implementation supports (log_base = e) and (log_base = 10) which is configured via
Constants.REPORT_LOG_BASE property. |
| TaxaCountModule |
TBD
|