Man pages for RIVM-IIV-Microbiome/biomeUtils
Utilities for microbiome analytics
| biomeUtils-package | 'biomeUtils' Package. |
| buildSeqTree | Build a phylogenetic tree |
| calculatePD | Calculate Faith's Phylogenetic Diversity |
| calculateQC | Calculate QC Metrics for Taxa and Samples |
| calculateTaxaFoldDifference | Calculate Fold Difference in Taxa Abundance |
| checkFilterEffect | Check Filter Effect |
| checkPolyphyletic | Check for Polyphyletic Taxa |
| cleanTaxonomy | Clean Taxonomy |
| comparePhyloseq | Compare Phyloseq Objects |
| fetchSequence | Retrieve Sequence from Phyloseq |
| filterPhyloseq | Filter Phyloseq Object |
| filterTaxaTotal | Filter Taxa Based on Total Data |
| findTopTaxa | Find the Top Taxa |
| FuentesIliGutData | FuentesIliGutData |
| genericUtilities | Generic utilities |
| getPhyloseqSlots | Get Phyloseq slots from Tibbles |
| getPrevalence | Get Prevalence and Taxonomy |
| getTaxaOverview | Get Overview of Taxa Abundances |
| getTaxaSummary | Get Taxa Summary at Specific Taxonomic Level |
| getTibble | Get tibble |
| getYCTheta | Yue and Clayton Measure of Dissimilarity |
| meltDistanceToTable | Convert Distance matrix to Data Frame |
| mutatePhyloseq | Mutating Slots of Phyloseq |
| pullPhyloseq | Pull Information from Phyloseq Object |
| readMergedMetaphlan | Read Merged Metaphlan Table |
| removeZeros | Remove Zeros |
| renameSampleVariables | Rename Sample Variables in Phyloseq Sample Data |
| saveData | Save data |
| saveSequence | Save Sequence |
| separateSampleColumn | Separate a Column in Phyloseq Sample Data |
| SprockettTHData | SprockettTHData |
| summarizeTaxonomicAssignments | Summarize Taxonomic Assignments |
| transformation | Common Transformations |
| trendAbundanceAssignment | Check Trend in Abundance and Taxonomic Assignment |
| uniqueness | Microbiota Uniqueness |
| uniteGenusSpeciesNames | Unite Genus Species Names |
| uniteSampleColumn | unite a Column in Phyloseq Sample Data |
