Package | Description |
---|---|
biolockj.module.diversity | |
biolockj.module.report.taxa | |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
Modifier and Type | Method and Description |
---|---|
protected TaxaLevelTable |
ShannonDiversity.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs) |
Modifier and Type | Method and Description |
---|---|
protected List<String> |
ShannonDiversity.filterTaxa(TaxaLevelTable inputData) |
protected TaxaLevelTable |
ShannonDiversity.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs) |
Modifier and Type | Method and Description |
---|---|
protected TaxaLevelTable |
AddPseudoCount.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs) |
protected TaxaLevelTable |
LogTransformTaxaTables.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Log transform the data
|
protected abstract TaxaLevelTable |
TransformTaxaTables.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Transform a table of values.
|
protected TaxaLevelTable |
NormalizeByReadsPerMillion.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs) |
protected TaxaLevelTable |
NormalizeTaxaTables.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1
|
Modifier and Type | Method and Description |
---|---|
protected List<String> |
TransformTaxaTables.filterSamples(TaxaLevelTable inputData)
Filter out any samples in which all values are 0.
|
protected List<String> |
TransformTaxaTables.filterTaxa(TaxaLevelTable inputData) |
protected TaxaLevelTable |
AddPseudoCount.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs) |
protected TaxaLevelTable |
LogTransformTaxaTables.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Log transform the data
|
protected abstract TaxaLevelTable |
TransformTaxaTables.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Transform a table of values.
|
protected TaxaLevelTable |
NormalizeByReadsPerMillion.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs) |
protected TaxaLevelTable |
NormalizeTaxaTables.transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1
|
Modifier and Type | Method and Description |
---|---|
static TaxaLevelTable |
TaxaUtil.readTaxaTable(File taxaTable)
Read a table of counts, formatted with samples as rows (ids in first column) and taxa as columns (ids in header).
|
Modifier and Type | Method and Description |
---|---|
static void |
TaxaUtil.writeDataToFile(File outFile,
List<String> sampleNames,
List<String> taxaNames,
TaxaLevelTable taxaCounts)
Write transformed data to file
|
static void |
TaxaUtil.writeDataToFile(File outFile,
TaxaLevelTable taxaCounts) |