Function reference • biomeUtils

All functions
`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
`checkAbundanceCutOffs()` `checkPrevalenceCutOffs()`	Check Filter Effect
`checkPolyphyletic`	Check for Polyphyletic Taxa
`cleanTaxonomy()`	Clean Taxonomy
`clusterASVs`	Cluster ASVs into Clusters
`comparePhyloseq()`	Compare Phyloseq Objects
`fetchSequence()`	Retrieve Sequence from Phyloseq
`filterSampleData()` `filterTaxaData()` `filterTaxaByNames()` `filterSampleByNames()`	Filter Phyloseq Object
`filterTaxaTotal`	Filter Taxa Based on Total Data
`findTopTaxa()`	Find the Top Taxa
`FuentesIliGutData`	FuentesIliGutData
`meltAbundance()` `transposeAbundance()`	Generic utilities
`getOtuTableFromTibble()` `getTaxaTableFromTibble()` `getSampleTableFromTibble()`	Get Phyloseq slots from Tibbles
`getPrevalence()`	Get Prevalence and Taxonomy
`getTaxaOverview()`	Get Overview of Taxa Abundances
`getTaxaSummary()`	Get Taxa Summary at Specific Taxonomic Level
`getAbundanceTibble()` `getTaxaTibble()` `getSampleTibble()`	Get tibble
`getYCTheta`	Yue and Clayton Measure of Dissimilarity
`meltDistanceToTable()`	Convert Distance matrix to Data Frame
`mutateSampleData()` `mutateTaxaTable()` `mutateAbundanceTable()`	Mutating Slots of Phyloseq
`pullSampleAbundance()` `pullTaxaAbundance()` `pullTaxaRank()`	Pull Information from Phyloseq Object
`readMergedMetaphlan()`	Read Merged Metaphlan Table
`removeZeros()`	Remove Zeros
`renameSampleVariables()`	Rename Sample Variables in Phyloseq Sample Data
`saveAbundanceData()` `saveTaxonomyData()` `saveSampleData()`	Save data
`saveSequence()`	Save Sequence
`separateSampleColumn()`	Separate a Column in Phyloseq Sample Data
`SprockettTHData`	SprockettTHData
`summarizeTaxonomicAssignments()`	Summarize Taxonomic Assignments
`getProportions()` `getCLR()`	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

Reference

All functions