Package: mia 1.13.23
Tuomas Borman
mia: Microbiome analysis
mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.
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mia.pdf |mia.html✨
mia/json (API)
NEWS
| # Install 'mia' in R: |
| install.packages('mia', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/microbiome/mia/issues
- GlobalPatterns - GlobalPatterns
- HintikkaXOData - HintikkaXOData
- Tengeler2020 - Tengeler2020
- dmn_se - Dmn_se
- enterotype - Enterotype
- esophagus - Esophagus
- peerj13075 - Peerj13075
On BioConductor:mia-1.13.0(bioc 3.20)mia-1.12.0(bioc 3.19)
Last updated 22 days agofrom:c17fa9f70f
Exports:addCCAaddClusteraddContaminantQCaddDivergenceaddDominantaddDPCoAaddHierarchyTreeaddMediationaddNMDSaddNotContaminantQCaddPerSampleDominantFeaturesaddPerSampleDominantTaxaaddRDAaddTaxonomyTreeagglomerateByPrevalenceagglomerateByRankagglomerateByRanksagglomerateByVariablebestDMNFitcalculateCCAcalculateDMNcalculateDMNgroupcalculateDPCoAcalculateJSDcalculateNMDScalculateOverlapcalculateRDAcalculateUnifraccheckTaxonomyclustercountDominantFeaturescountDominantTaxaestimateDivergenceestimateDiversityestimateDominanceestimateEvennessestimateFaithestimateRichnessfull_joingetBestDMNFitgetCCAgetCrossAssociationgetDMNgetDominantgetDPCoAgetExperimentCrossAssociationgetExperimentCrossCorrelationgetHierarchyTreegetMediationgetNMDSgetPrevalencegetPrevalentgetPrevalentAbundancegetPrevalentFeaturesgetPrevalentTaxagetRaregetRareFeaturesgetRareTaxagetRDAgetTaxonomyLabelsgetTaxonomyRanksgetTopgetTopFeaturesgetTopTaxagetUniquegetUniqueFeaturesgetUniqueTaxaIdTaxaToDataFrameimportBIOMimportHUMAnNimportMetaPhlAnimportMothurimportQIIME2importQZAinner_joinisContaminantisNotContaminantleft_joinloadFromBiomloadFromHumannloadFromMetaphlanloadFromMothurloadFromQIIME2makePhyloseqFromTreeSEmakePhyloseqFromTreeSummarizedExperimentmakeTreeSEFromBiommakeTreeSEFromDADA2makeTreeSEFromPhyloseqmakeTreeSummarizedExperimentFromBiommakeTreeSummarizedExperimentFromDADA2makeTreeSummarizedExperimentFromPhyloseqmapTaxonomymeltAssaymeltSEmergeColsmergeFeaturesmergeFeaturesByPrevalencemergeFeaturesByRankmergeRowsmergeSamplesmergeSEsperformDMNgroupCVperSampleDominantFeaturesperSampleDominantTaxaplotNMDSrarefyAssayreadQZArelabundancerelabundance<-relAbundanceCountsright_joinrunCCArunDMNrunDPCoArunJSDrunNMDSrunOverlaprunRDArunUnifracsetTaxonomyRankssplitByRankssplitOnsubsampleCountssubsetByPrevalentsubsetByPrevalentFeaturessubsetByPrevalentTaxasubsetByRaresubsetByRareFeaturessubsetByRareTaxasubsetFeaturessubsetSamplessubsetTaxasummarizeDominancesummaryTAXONOMY_RANKStaxonomyRankEmptytaxonomyRankstaxonomyTreetestExperimentCrossAssociationtestExperimentCrossCorrelationtransformAssaytransformCountstransformFeaturestransformSamplesunsplitByRanksunsplitOnZTransform
Dependencies:abindapeaskpassbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblusterbootbslibcachemCairocheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphIRangesirlbaisobandjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclelme4lpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmediationmemoisemgcvmimeminqaMultiAssayExperimentmunsellmvtnormnlmenloptrnnetopensslopenxlsxpermutepheatmappillarpkgconfigplyrpngpurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbiomRColorBrewerRcppRcppAnnoyRcppEigenRcppHNSWRcppMLRcppParallelRcppProgressreshape2rjsonrlangrmarkdownrpartRSpectrarstudioapirsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscuttleSingleCellExperimentsitmoslamsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttidytreetinytextreeioTreeSummarizedExperimentUCSC.utilsutf8uwotvctrsveganviporviridisviridisLitewithrxfunXVectoryamlyulab.utilszipzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'mia' Package. | mia-package mia |
| Clustering wrapper | addCluster addCluster,SummarizedExperiment-method |
| Estimate divergence | addDivergence addDivergence,SummarizedExperiment-method |
| Agglomerate or merge data using taxonomic information | agglomerate-methods agglomerateByPrevalence agglomerateByPrevalence,SummarizedExperiment-method agglomerateByRank agglomerateByRank,SingleCellExperiment-method agglomerateByRank,SummarizedExperiment-method agglomerateByRank,TreeSummarizedExperiment-method agglomerateByRanks agglomerateByRanks,SingleCellExperiment-method agglomerateByRanks,SummarizedExperiment-method agglomerateByRanks,TreeSummarizedExperiment-method agglomerateByVariable agglomerateByVariable,SummarizedExperiment-method agglomerateByVariable,TreeSummarizedExperiment-method splitByRanks unsplitByRanks unsplitByRanks,SingleCellExperiment-method unsplitByRanks,TreeSummarizedExperiment-method |
| Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data | bestDMNFit bestDMNFit,SummarizedExperiment-method calculateDMN calculateDMN,ANY-method calculateDMN,SummarizedExperiment-method calculateDMNgroup calculateDMNgroup,ANY-method calculateDMNgroup,SummarizedExperiment-method getBestDMNFit getBestDMNFit,SummarizedExperiment-method getDMN getDMN,SummarizedExperiment-method performDMNgroupCV performDMNgroupCV,ANY-method performDMNgroupCV,SummarizedExperiment-method runDMN |
| Calculate the Jensen-Shannon Divergence | calculateJSD calculateJSD,ANY-method calculateJSD,SummarizedExperiment-method runJSD |
| Estimate overlap | calculateOverlap calculateOverlap,SummarizedExperiment-method runOverlap runOverlap,SummarizedExperiment-method |
| Calculate weighted or unweighted (Fast) Unifrac distance | calculateUnifrac calculateUnifrac,ANY,phylo-method calculateUnifrac,TreeSummarizedExperiment,missing-method runUnifrac |
| These functions will be deprecated. Please use other functions instead. | addPerSampleDominantFeatures addPerSampleDominantFeatures,SummarizedExperiment-method addPerSampleDominantTaxa addPerSampleDominantTaxa,SummarizedExperiment-method addTaxonomyTree addTaxonomyTree,SummarizedExperiment-method cluster cluster,SummarizedExperiment-method countDominantFeatures countDominantFeatures,SummarizedExperiment-method countDominantTaxa countDominantTaxa,SummarizedExperiment-method deprecate estimateDivergence estimateDivergence,SummarizedExperiment-method full_join full_join,ANY-method getExperimentCrossAssociation getExperimentCrossAssociation,MultiAssayExperiment-method getExperimentCrossAssociation,SummarizedExperiment-method getExperimentCrossCorrelation getExperimentCrossCorrelation,ANY-method getPrevalentFeatures getPrevalentFeatures,ANY-method getPrevalentFeatures,SummarizedExperiment-method getPrevalentTaxa getPrevalentTaxa,ANY-method getPrevalentTaxa,SummarizedExperiment-method getRareFeatures getRareFeatures,ANY-method getRareFeatures,SummarizedExperiment-method getRareTaxa getRareTaxa,ANY-method getRareTaxa,SummarizedExperiment-method getTopFeatures getTopFeatures,SummarizedExperiment-method getTopTaxa getTopTaxa,SummarizedExperiment-method getUniqueFeatures getUniqueFeatures,SummarizedExperiment-method getUniqueTaxa getUniqueTaxa,SummarizedExperiment-method inner_join inner_join,ANY-method left_join left_join,ANY-method loadFromBiom loadFromHumann loadFromMetaphlan loadFromMothur loadFromQIIME2 meltAssay meltAssay,SummarizedExperiment-method mergeCols mergeCols,SummarizedExperiment-method mergeCols,TreeSummarizedExperiment-method mergeFeatures mergeFeatures,SummarizedExperiment-method mergeFeatures,TreeSummarizedExperiment-method mergeFeaturesByPrevalence mergeFeaturesByPrevalence,SummarizedExperiment-method mergeFeaturesByRank mergeFeaturesByRank,SingleCellExperiment-method mergeFeaturesByRank,SummarizedExperiment-method mergeFeaturesByRank,TreeSummarizedExperiment-method mergeRows mergeRows,SummarizedExperiment-method mergeRows,TreeSummarizedExperiment-method mergeSamples mergeSamples,SummarizedExperiment-method mergeSamples,TreeSummarizedExperiment-method perSampleDominantFeatures perSampleDominantFeatures,SummarizedExperiment-method perSampleDominantTaxa perSampleDominantTaxa,SummarizedExperiment-method plotNMDS readQZA relAbundanceCounts relAbundanceCounts,SummarizedExperiment-method right_join right_join,ANY-method subsampleCounts subsampleCounts,SummarizedExperiment-method subsetByPrevalentFeatures subsetByPrevalentFeatures,ANY-method subsetByPrevalentTaxa subsetByPrevalentTaxa,ANY-method subsetByRareFeatures subsetByRareFeatures,ANY-method subsetByRareTaxa subsetByRareTaxa,ANY-method taxonomyTree taxonomyTree,SummarizedExperiment-method testExperimentCrossAssociation testExperimentCrossAssociation,ANY-method testExperimentCrossCorrelation testExperimentCrossCorrelation,ANY-method transformCounts transformFeatures transformFeatures,SummarizedExperiment-method transformSamples transformSamples,SummarizedExperiment-method ZTransform ZTransform,SummarizedExperiment-method |
| dmn_se | dmn_se twins |
| enterotype | enterotype |
| esophagus | esophagus |
| Estimate (alpha) diversity measures | estimateDiversity estimateDiversity,SummarizedExperiment-method estimateDiversity,TreeSummarizedExperiment-method estimateFaith estimateFaith,SummarizedExperiment,phylo-method estimateFaith,TreeSummarizedExperiment,missing-method |
| Estimate dominance measures | estimateDominance estimateDominance,SummarizedExperiment-method |
| Estimate Evenness measures | estimateEvenness estimateEvenness,SummarizedExperiment-method |
| Estimate richness measures | estimateRichness estimateRichness,SummarizedExperiment-method |
| Calculate correlations between features of two experiments. | getCrossAssociation getCrossAssociation,MultiAssayExperiment-method getCrossAssociation,SummarizedExperiment-method |
| Get dominant taxa | addDominant addDominant,SummarizedExperiment-method getDominant getDominant,SummarizedExperiment-method |
| Perform mediation analysis | addMediation addMediation,SummarizedExperiment-method getMediation getMediation,SummarizedExperiment-method |
| Calculation prevalence information for features across samples | getPrevalence getPrevalence,ANY-method getPrevalence,SummarizedExperiment-method getPrevalent getPrevalent,ANY-method getPrevalent,SummarizedExperiment-method getPrevalentAbundance getPrevalentAbundance,ANY-method getPrevalentAbundance,SummarizedExperiment-method getRare getRare,ANY-method getRare,SummarizedExperiment-method subsetByPrevalent subsetByPrevalent,SummarizedExperiment-method subsetByRare subsetByRare,SummarizedExperiment-method |
| GlobalPatterns | GlobalPatterns |
| Calculate hierarchy tree | addHierarchyTree addHierarchyTree,SummarizedExperiment-method getHierarchyTree getHierarchyTree,SummarizedExperiment-method hierarchy-tree |
| HintikkaXOData | HintikkaXOData |
| Import HUMAnN results to 'TreeSummarizedExperiment' | importHUMAnN |
| Import Metaphlan results to 'TreeSummarizedExperiment' | importMetaPhlAn |
| Import Mothur results as a 'TreeSummarizedExperiment' | importMothur |
| Import QIIME2 results to 'TreeSummarizedExperiment' | importQIIME2 importQZA |
| decontam functions | addContaminantQC addContaminantQC,SummarizedExperiment-method addNotContaminantQC addNotContaminantQC,SummarizedExperiment-method isContaminant isContaminant,SummarizedExperiment-method isNotContaminant,SummarizedExperiment-method |
| Create a phyloseq object from a TreeSummarizedExperiment object | makePhyloseqFromTreeSE makePhyloseqFromTreeSE,SummarizedExperiment-method makePhyloseqFromTreeSE,TreeSummarizedExperiment-method makePhyloseqFromTreeSummarizedExperiment makePhyloseqFromTreeSummarizedExperiment,ANY-method |
| Loading a biom file | importBIOM makeTreeSEFromBiom makeTreeSummarizedExperimentFromBiom |
| Coerce 'DADA2' results to 'TreeSummarizedExperiment' | makeTreeSEFromDADA2 makeTreeSummarizedExperimentFromDADA2 |
| Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment' | makeTreeSEFromPhyloseq makeTreeSummarizedExperimentFromPhyloseq makeTreeSummarizedExperimentFromPhyloseq,ANY-method |
| Converting a 'SummarizedExperiment' object into a long data.frame | meltSE meltSE,SummarizedExperiment-method |
| Merge SE objects into single SE object. | mergeSEs mergeSEs,list-method mergeSEs,SimpleList-method mergeSEs,SummarizedExperiment-method |
| mia datasets | mia-datasets |
| peerj13075 | peerj13075 |
| Subsample Counts | rarefyAssay rarefyAssay,SummarizedExperiment-method |
| Getter / setter for relative abundance data | relabundance relabundance,SummarizedExperiment-method relabundance<- relabundance<-,SummarizedExperiment-method |
| Canonical Correspondence Analysis and Redundancy Analysis | addCCA addCCA,SingleCellExperiment-method addRDA addRDA,SingleCellExperiment-method calculateCCA calculateRDA getCCA getCCA,ANY-method getCCA,SummarizedExperiment-method getRDA getRDA,ANY-method getRDA,SummarizedExperiment-method runCCA runRDA |
| Calculation of Double Principal Correspondance analysis | addDPCoA calculateDPCoA getDPCoA getDPCoA,ANY,ANY-method getDPCoA,TreeSummarizedExperiment,missing-method runDPCoA |
| Perform non-metric MDS on sample-level data | addNMDS calculateNMDS getNMDS getNMDS,ANY-method getNMDS,SingleCellExperiment-method getNMDS,SummarizedExperiment-method runNMDS |
| Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable | splitOn splitOn,SingleCellExperiment-method splitOn,SummarizedExperiment-method splitOn,TreeSummarizedExperiment-method unsplitOn unsplitOn,list-method unsplitOn,SimpleList-method unsplitOn,SingleCellExperiment-method |
| Subset functions | subsetFeatures subsetFeatures,SummarizedExperiment-method subsetSamples subsetSamples,SummarizedExperiment-method subsetTaxa subsetTaxa,SummarizedExperiment-method |
| Summarizing microbiome data | getTop getTop,SummarizedExperiment-method getUnique getUnique,SummarizedExperiment-method summaries summarizeDominance summarizeDominance,SummarizedExperiment-method summary,SummarizedExperiment-method |
| Functions for accessing taxonomic data stored in 'rowData'. | checkTaxonomy checkTaxonomy,SummarizedExperiment-method getTaxonomyLabels getTaxonomyLabels,SummarizedExperiment-method getTaxonomyRanks IdTaxaToDataFrame mapTaxonomy mapTaxonomy,SummarizedExperiment-method setTaxonomyRanks taxonomy-methods taxonomyRankEmpty taxonomyRankEmpty,SummarizedExperiment-method taxonomyRanks taxonomyRanks,SummarizedExperiment-method TAXONOMY_RANKS |
| Tengeler2020 | Tengeler2020 |
| Transform assay | transformAssay transformAssay,SummarizedExperiment-method |