Microbiome analysis
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Documentation for package ‘mia’ version 1.15.20
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A B C D E F G H I L M P R S T U Z
| mia-package | 'mia' Package. |
-- A --
| addAbundanceClass | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| addAbundanceClass-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| addAlpha | Estimate alpha diversity indices |
| addAlpha-method | Estimate alpha diversity indices |
| addCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| addCCA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| addCluster | Clustering wrapper |
| addCluster-method | Clustering wrapper |
| addContaminantQC | decontam functions |
| addContaminantQC-method | decontam functions |
| addDissimilarity | Calculate dissimilarities |
| addDissimilarity-method | Calculate dissimilarities |
| addDivergence | Estimate divergence |
| addDivergence-method | Estimate divergence |
| addDominant | Get dominant taxa |
| addDominant-method | Get dominant taxa |
| addDPCoA | Calculation of Double Principal Correspondance analysis |
| addHierarchyTree | Calculate hierarchy tree |
| addHierarchyTree-method | Calculate hierarchy tree |
| addLDA | Latent Dirichlet Allocation |
| addLDA-method | Latent Dirichlet Allocation |
| addMediation | Perform mediation analysis |
| addMediation-method | Perform mediation analysis |
| addNMDS | Perform non-metric MDS on sample-level data |
| addNMF | Non-negative Matrix Factorization |
| addNMF-method | Non-negative Matrix Factorization |
| addNotContaminantQC | decontam functions |
| addNotContaminantQC-method | decontam functions |
| addPERMANOVA | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance) |
| addPERMANOVA-method | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance) |
| addPerSampleDominantFeatures | These functions will be deprecated. Please use other functions instead. |
| addPerSampleDominantFeatures-method | These functions will be deprecated. Please use other functions instead. |
| addPerSampleDominantTaxa | These functions will be deprecated. Please use other functions instead. |
| addPerSampleDominantTaxa-method | These functions will be deprecated. Please use other functions instead. |
| addPrevalence | Calculation prevalence information for features across samples |
| addPrevalence-method | Calculation prevalence information for features across samples |
| addRDA | Canonical Correspondence Analysis and Redundancy Analysis |
| addRDA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| addTaxonomyTree | These functions will be deprecated. Please use other functions instead. |
| addTaxonomyTree-method | These functions will be deprecated. Please use other functions instead. |
| agglomerate-methods | Agglomerate data using taxonomic information or other grouping |
| agglomerateByPrevalence | Agglomerate data based on population prevalence |
| agglomerateByPrevalence-method | Agglomerate data based on population prevalence |
| agglomerateByRank | Agglomerate data using taxonomic information or other grouping |
| agglomerateByRank-method | Agglomerate data using taxonomic information or other grouping |
| agglomerateByRanks | Agglomerate data using taxonomic information or other grouping |
| agglomerateByRanks-method | Agglomerate data using taxonomic information or other grouping |
| agglomerateByVariable | Agglomerate data using taxonomic information or other grouping |
| agglomerateByVariable-method | Agglomerate data using taxonomic information or other grouping |
-- B --
| bestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| bestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
-- C --
| calculateCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| calculateDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDMNgroup | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDMNgroup-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDPCoA | Calculation of Double Principal Correspondance analysis |
| calculateJSD | These functions will be deprecated. Please use other functions instead. |
| calculateJSD-method | These functions will be deprecated. Please use other functions instead. |
| calculateNMDS | Perform non-metric MDS on sample-level data |
| calculateOverlap | These functions will be deprecated. Please use other functions instead. |
| calculateOverlap-method | These functions will be deprecated. Please use other functions instead. |
| calculateRDA | Canonical Correspondence Analysis and Redundancy Analysis |
| calculateUnifrac | These functions will be deprecated. Please use other functions instead. |
| calculateUnifrac-method | These functions will be deprecated. Please use other functions instead. |
| checkTaxonomy | Functions for accessing taxonomic data stored in 'rowData'. |
| checkTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'. |
| cluster | These functions will be deprecated. Please use other functions instead. |
| cluster-method | These functions will be deprecated. Please use other functions instead. |
| convertFromBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results |
| convertFromDADA2 | Create a 'TreeSummarizedExperiment' object from 'DADA2' results |
| convertFromPhyloseq | Create a 'TreeSummarizedExperiment' object from a phyloseq object |
| convertToBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results |
| convertToBIOM-method | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results |
| convertToPhyloseq | Create a 'TreeSummarizedExperiment' object from a phyloseq object |
| convertToPhyloseq-method | Create a 'TreeSummarizedExperiment' object from a phyloseq object |
| countDominantFeatures | These functions will be deprecated. Please use other functions instead. |
| countDominantFeatures-method | These functions will be deprecated. Please use other functions instead. |
| countDominantTaxa | These functions will be deprecated. Please use other functions instead. |
| countDominantTaxa-method | These functions will be deprecated. Please use other functions instead. |
-- D --
| deprecate | These functions will be deprecated. Please use other functions instead. |
| dmn_se | Twins' microbiome data from 278 individuals |
-- E --
| enterotype | Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing |
| esophagus | Human esophageal community from 3 individuals |
| estimateDivergence | These functions will be deprecated. Please use other functions instead. |
| estimateDivergence-method | These functions will be deprecated. Please use other functions instead. |
| estimateDiversity | These functions will be deprecated. Please use other functions instead. |
| estimateDiversity-method | These functions will be deprecated. Please use other functions instead. |
| estimateDominance | These functions will be deprecated. Please use other functions instead. |
| estimateDominance-method | These functions will be deprecated. Please use other functions instead. |
| estimateEvenness | These functions will be deprecated. Please use other functions instead. |
| estimateEvenness-method | These functions will be deprecated. Please use other functions instead. |
| estimateFaith | These functions will be deprecated. Please use other functions instead. |
| estimateFaith-method | These functions will be deprecated. Please use other functions instead. |
| estimateRichness | These functions will be deprecated. Please use other functions instead. |
| estimateRichness-method | These functions will be deprecated. Please use other functions instead. |
-- F --
| full_join | These functions will be deprecated. Please use other functions instead. |
| full_join-method | These functions will be deprecated. Please use other functions instead. |
-- G --
| getAbundanceClass | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getAbundanceClass-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getAlpha | Estimate alpha diversity indices |
| getAlpha-method | Estimate alpha diversity indices |
| getBestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getBestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| getCCA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| getConditionallyLowAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getConditionallyLowAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getCrossAssociation | Calculate correlations between features of two experiments. |
| getCrossAssociation-method | Calculate correlations between features of two experiments. |
| getDissimilarity | Calculate dissimilarities |
| getDissimilarity-method | Calculate dissimilarities |
| getDivergence | Estimate divergence |
| getDivergence-method | Estimate divergence |
| getDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getDominant | Get dominant taxa |
| getDominant-method | Get dominant taxa |
| getDPCoA | Calculation of Double Principal Correspondance analysis |
| getDPCoA-method | Calculation of Double Principal Correspondance analysis |
| getExperimentCrossAssociation | These functions will be deprecated. Please use other functions instead. |
| getExperimentCrossAssociation-method | These functions will be deprecated. Please use other functions instead. |
| getExperimentCrossCorrelation | These functions will be deprecated. Please use other functions instead. |
| getExperimentCrossCorrelation-method | These functions will be deprecated. Please use other functions instead. |
| getHierarchyTree | Calculate hierarchy tree |
| getHierarchyTree-method | Calculate hierarchy tree |
| getLDA | Latent Dirichlet Allocation |
| getLDA-method | Latent Dirichlet Allocation |
| getLowAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getLowAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getMediation | Perform mediation analysis |
| getMediation-method | Perform mediation analysis |
| getNMDS | Perform non-metric MDS on sample-level data |
| getNMDS-method | Perform non-metric MDS on sample-level data |
| getNMF | Non-negative Matrix Factorization |
| getNMF-method | Non-negative Matrix Factorization |
| getPermanentlyLowAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getPermanentlyLowAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare. |
| getPERMANOVA | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance) |
| getPERMANOVA-method | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance) |
| getPrevalence | Calculation prevalence information for features across samples |
| getPrevalence-method | Calculation prevalence information for features across samples |
| getPrevalent | Calculation prevalence information for features across samples |
| getPrevalent-method | Calculation prevalence information for features across samples |
| getPrevalentAbundance | Calculation prevalence information for features across samples |
| getPrevalentAbundance-method | Calculation prevalence information for features across samples |
| getPrevalentFeatures | These functions will be deprecated. Please use other functions instead. |
| getPrevalentFeatures-method | These functions will be deprecated. Please use other functions instead. |
| getPrevalentTaxa | These functions will be deprecated. Please use other functions instead. |
| getPrevalentTaxa-method | These functions will be deprecated. Please use other functions instead. |
| getRare | Calculation prevalence information for features across samples |
| getRare-method | Calculation prevalence information for features across samples |
| getRareFeatures | These functions will be deprecated. Please use other functions instead. |
| getRareFeatures-method | These functions will be deprecated. Please use other functions instead. |
| getRareTaxa | These functions will be deprecated. Please use other functions instead. |
| getRareTaxa-method | These functions will be deprecated. Please use other functions instead. |
| getRDA | Canonical Correspondence Analysis and Redundancy Analysis |
| getRDA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| getTaxonomyLabels | Functions for accessing taxonomic data stored in 'rowData'. |
| getTaxonomyLabels-method | Functions for accessing taxonomic data stored in 'rowData'. |
| getTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'. |
| getTop | Summarizing microbiome data |
| getTop-method | Summarizing microbiome data |
| getTopFeatures | These functions will be deprecated. Please use other functions instead. |
| getTopFeatures-method | These functions will be deprecated. Please use other functions instead. |
| getTopTaxa | These functions will be deprecated. Please use other functions instead. |
| getTopTaxa-method | These functions will be deprecated. Please use other functions instead. |
| getUnique | Summarizing microbiome data |
| getUnique-method | Summarizing microbiome data |
| getUniqueFeatures | These functions will be deprecated. Please use other functions instead. |
| getUniqueFeatures-method | These functions will be deprecated. Please use other functions instead. |
| getUniqueTaxa | These functions will be deprecated. Please use other functions instead. |
| getUniqueTaxa-method | These functions will be deprecated. Please use other functions instead. |
| GlobalPatterns | Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. |
-- H --
| hierarchy-tree | Calculate hierarchy tree |
| HintikkaXOData | Multiomics dataset from 40 rat samples |
-- I --
| IdTaxaToDataFrame | Functions for accessing taxonomic data stored in 'rowData'. |
| importBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results |
| importHUMAnN | Import HUMAnN results to 'TreeSummarizedExperiment' |
| importMetaPhlAn | Import Metaphlan results to 'TreeSummarizedExperiment' |
| importMothur | Import Mothur results as a 'TreeSummarizedExperiment' |
| importQIIME2 | Import QIIME2 results to 'TreeSummarizedExperiment' |
| importQZA | Import QIIME2 results to 'TreeSummarizedExperiment' |
| importTaxpasta | Import taxpasta-specific BIOM results to 'TreeSummarizedExperiment' |
| inner_join | These functions will be deprecated. Please use other functions instead. |
| inner_join-method | These functions will be deprecated. Please use other functions instead. |
| isContaminant | decontam functions |
| isContaminant-method | decontam functions |
| isNotContaminant-method | decontam functions |
-- L --
| left_join | These functions will be deprecated. Please use other functions instead. |
| left_join-method | These functions will be deprecated. Please use other functions instead. |
| loadFromBiom | These functions will be deprecated. Please use other functions instead. |
| loadFromHumann | These functions will be deprecated. Please use other functions instead. |
| loadFromMetaphlan | These functions will be deprecated. Please use other functions instead. |
| loadFromMothur | These functions will be deprecated. Please use other functions instead. |
| loadFromQIIME2 | These functions will be deprecated. Please use other functions instead. |
-- M --
| makePhyloseqFromTreeSE | These functions will be deprecated. Please use other functions instead. |
| makePhyloseqFromTreeSE-method | These functions will be deprecated. Please use other functions instead. |
| makePhyloseqFromTreeSummarizedExperiment | These functions will be deprecated. Please use other functions instead. |
| makePhyloseqFromTreeSummarizedExperiment-method | These functions will be deprecated. Please use other functions instead. |
| makeTreeSEFromBiom | These functions will be deprecated. Please use other functions instead. |
| makeTreeSEFromDADA2 | These functions will be deprecated. Please use other functions instead. |
| makeTreeSEFromPhyloseq | These functions will be deprecated. Please use other functions instead. |
| makeTreeSummarizedExperimentFromBiom | These functions will be deprecated. Please use other functions instead. |
| makeTreeSummarizedExperimentFromDADA2 | These functions will be deprecated. Please use other functions instead. |
| makeTreeSummarizedExperimentFromPhyloseq | These functions will be deprecated. Please use other functions instead. |
| makeTreeSummarizedExperimentFromPhyloseq-method | These functions will be deprecated. Please use other functions instead. |
| mapTaxonomy | Functions for accessing taxonomic data stored in 'rowData'. |
| mapTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'. |
| meltAssay | These functions will be deprecated. Please use other functions instead. |
| meltAssay-method | These functions will be deprecated. Please use other functions instead. |
| meltSE | Converting a 'SummarizedExperiment' object into a long data.frame |
| meltSE-method | Converting a 'SummarizedExperiment' object into a long data.frame |
| mergeCols | These functions will be deprecated. Please use other functions instead. |
| mergeCols-method | These functions will be deprecated. Please use other functions instead. |
| mergeFeatures | These functions will be deprecated. Please use other functions instead. |
| mergeFeatures-method | These functions will be deprecated. Please use other functions instead. |
| mergeFeaturesByPrevalence | These functions will be deprecated. Please use other functions instead. |
| mergeFeaturesByPrevalence-method | These functions will be deprecated. Please use other functions instead. |
| mergeFeaturesByRank | These functions will be deprecated. Please use other functions instead. |
| mergeFeaturesByRank-method | These functions will be deprecated. Please use other functions instead. |
| mergeRows | These functions will be deprecated. Please use other functions instead. |
| mergeRows-method | These functions will be deprecated. Please use other functions instead. |
| mergeSamples | These functions will be deprecated. Please use other functions instead. |
| mergeSamples-method | These functions will be deprecated. Please use other functions instead. |
| mergeSEs | Merge SE objects into single SE object. |
| mergeSEs-method | Merge SE objects into single SE object. |
| mia | 'mia' Package. |
| mia-datasets | mia datasets |
-- P --
| peerj13075 | Skin microbial profiles 58 genetically unrelated individuals |
| performDMNgroupCV | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| performDMNgroupCV-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| perSampleDominantFeatures | These functions will be deprecated. Please use other functions instead. |
| perSampleDominantFeatures-method | These functions will be deprecated. Please use other functions instead. |
| perSampleDominantTaxa | These functions will be deprecated. Please use other functions instead. |
| perSampleDominantTaxa-method | These functions will be deprecated. Please use other functions instead. |
| plotNMDS | These functions will be deprecated. Please use other functions instead. |
-- R --
| rarefyAssay | Subsample Counts |
| rarefyAssay-method | Subsample Counts |
| readQZA | These functions will be deprecated. Please use other functions instead. |
| relabundance | These functions will be deprecated. Please use other functions instead. |
| relabundance-method | These functions will be deprecated. Please use other functions instead. |
| relabundance<- | These functions will be deprecated. Please use other functions instead. |
| relabundance<--method | These functions will be deprecated. Please use other functions instead. |
| relAbundanceCounts | These functions will be deprecated. Please use other functions instead. |
| relAbundanceCounts-method | These functions will be deprecated. Please use other functions instead. |
| right_join | These functions will be deprecated. Please use other functions instead. |
| right_join-method | These functions will be deprecated. Please use other functions instead. |
| runCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| runDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| runDPCoA | Calculation of Double Principal Correspondance analysis |
| runJSD | These functions will be deprecated. Please use other functions instead. |
| runJSD-method | These functions will be deprecated. Please use other functions instead. |
| runNMDS | Perform non-metric MDS on sample-level data |
| runOverlap | These functions will be deprecated. Please use other functions instead. |
| runOverlap-method | These functions will be deprecated. Please use other functions instead. |
| runRDA | Canonical Correspondence Analysis and Redundancy Analysis |
| runUnifrac | These functions will be deprecated. Please use other functions instead. |
-- S --
| setTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'. |
| splitByRanks | Agglomerate data using taxonomic information or other grouping |
| splitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| splitOn-method | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| subsampleCounts | These functions will be deprecated. Please use other functions instead. |
| subsampleCounts-method | These functions will be deprecated. Please use other functions instead. |
| subsetByPrevalent | Calculation prevalence information for features across samples |
| subsetByPrevalent-method | Calculation prevalence information for features across samples |
| subsetByPrevalentFeatures | These functions will be deprecated. Please use other functions instead. |
| subsetByPrevalentFeatures-method | These functions will be deprecated. Please use other functions instead. |
| subsetByPrevalentTaxa | These functions will be deprecated. Please use other functions instead. |
| subsetByPrevalentTaxa-method | These functions will be deprecated. Please use other functions instead. |
| subsetByRare | Calculation prevalence information for features across samples |
| subsetByRare-method | Calculation prevalence information for features across samples |
| subsetByRareFeatures | These functions will be deprecated. Please use other functions instead. |
| subsetByRareFeatures-method | These functions will be deprecated. Please use other functions instead. |
| subsetByRareTaxa | These functions will be deprecated. Please use other functions instead. |
| subsetByRareTaxa-method | These functions will be deprecated. Please use other functions instead. |
| subsetFeatures | These functions will be deprecated. Please use other functions instead. |
| subsetFeatures-method | These functions will be deprecated. Please use other functions instead. |
| subsetSamples | These functions will be deprecated. Please use other functions instead. |
| subsetSamples-method | These functions will be deprecated. Please use other functions instead. |
| subsetTaxa | These functions will be deprecated. Please use other functions instead. |
| subsetTaxa-method | These functions will be deprecated. Please use other functions instead. |
| summarizeDominance | Summarizing microbiome data |
| summarizeDominance-method | Summarizing microbiome data |
| summary | Summarizing microbiome data |
| summary-method | Summarizing microbiome data |
-- T --
| taxonomy-methods | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRankEmpty | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRankEmpty-method | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRanks-method | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyTree | These functions will be deprecated. Please use other functions instead. |
| taxonomyTree-method | These functions will be deprecated. Please use other functions instead. |
| Tengeler2020 | Gut microbiota profiles of 27 individuals with ADHD and healthy controls |
| testExperimentCrossAssociation | These functions will be deprecated. Please use other functions instead. |
| testExperimentCrossAssociation-method | These functions will be deprecated. Please use other functions instead. |
| testExperimentCrossCorrelation | These functions will be deprecated. Please use other functions instead. |
| testExperimentCrossCorrelation-method | These functions will be deprecated. Please use other functions instead. |
| Tito2024QMP | Fecal microbiota samples from 589 patients across different colorectal cancer stages |
| transformAssay | Transform assay |
| transformAssay-method | Transform assay |
| transformCounts | These functions will be deprecated. Please use other functions instead. |
| transformFeatures | These functions will be deprecated. Please use other functions instead. |
| transformFeatures-method | These functions will be deprecated. Please use other functions instead. |
| transformSamples | These functions will be deprecated. Please use other functions instead. |
| transformSamples-method | These functions will be deprecated. Please use other functions instead. |
| twins | Twins' microbiome data from 278 individuals |
-- U --
| unsplitByRanks | Agglomerate data using taxonomic information or other grouping |
| unsplitByRanks-method | Agglomerate data using taxonomic information or other grouping |
| unsplitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| unsplitOn-method | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
-- Z --
| ZTransform | These functions will be deprecated. Please use other functions instead. |
| ZTransform-method | These functions will be deprecated. Please use other functions instead. |