Package: mia 1.21.3

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.

Authors:Tuomas Borman [aut, cre], Felix G.M. Ernst [aut], Sudarshan A. Shetty [aut], Leo Lahti [aut], Yang Cao [ctb], Nathan D. Olson [ctb], Levi Waldron [ctb], Marcel Ramos [ctb], Héctor Corrada Bravo [ctb], Jayaram Kancherla [ctb], Domenick Braccia [ctb], Basil Courbayre [ctb], Geraldson Muluh [ctb], Giulio Benedetti [ctb], Moritz Emanuel Beber [ctb], Chouaib Benchraka [ctb], Akewak Jeba [ctb], Himmi Lindgren [ctb], Noah De Gunst [ctb], Théotime Pralas [ctb], Shadman Ishraq [ctb], Eineje Ameh [ctb], Artur Sannikov [ctb], Hervé Pagès [ctb], Rajesh Shigdel [ctb], Katariina Pärnänen [ctb], Pande Erawijantari [ctb], Danielle Callan [ctb], Sam Hillman [ctb], Jesse Pasanen [ctb], Eetu Tammi [ctb], Aituar Bektanov [ctb], Rasmus Hindström [ctb], Sabuj Bhowmick [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mia/json (API)

# 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

Pkgdown/docs site:https://microbiome.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

dmn_se - Twins' microbiome data from 278 individuals
enterotype - Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing
esophagus - Human esophageal community from 3 individuals
GlobalPatterns - Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.
HintikkaXOData - Multiomics dataset from 40 rat samples
ibdmdb - IBDMDB 2-omic demo dataset
peerj13075 - Skin microbial profiles 58 genetically unrelated individuals
Tengeler2020 - Gut microbiota profiles of 27 individuals with ADHD and healthy controls
Tito2024QMP - Fecal microbiota samples from 589 patients across different colorectal cancer stages

On BioConductor:mia-1.21.3(bioc 3.24)mia-1.20.0(bioc 3.23)

microbiome software dataimport analysis bioconductor cpp

11.65 score 57 stars 8 packages 964 scripts 1 mentions 180 exports 119 dependencies

Last updated from:fcd07419d8. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	475
linux-devel-arm64	NOTE	1418
linux-devel-x86_64	NOTE	1585
source / vignettes	OK	602
linux-release-arm64	NOTE	1526
linux-release-x86_64	NOTE	1615
macos-release-arm64	NOTE	1035
macos-release-x86_64	NOTE	2873
macos-oldrel-arm64	NOTE	1428
macos-oldrel-x86_64	NOTE	2492
windows-devel	NOTE	1839
windows-release	NOTE	1965
windows-oldrel	NOTE	1859
wasm-release	OK	916

Exports:addAbundanceClass addAlpha addCCA addCluster addContaminantQC addDissimilarity addDivergence addDominant addDPCoA addHierarchyTree addJointRPCA addLDA addMDS addMediation addNMDS addNMF addNotContaminantQC addPERMANOVA addPerSampleDominantFeatures addPerSampleDominantTaxa addPrevalence addPrevalentAbundance addRDA addRPCA addTaxonomyTree agglomerateByModule agglomerateByPrevalence agglomerateByRank agglomerateByRanks agglomerateByVariable bestDMNFit calculateCCA calculateDMN calculateDMNgroup calculateDPCoA calculateJSD calculateNMDS calculateOverlap calculateRDA calculateUnifrac checkTaxonomy cluster convertFromBIOM convertFromDADA2 convertFromPhyloseq convertToBIOM convertToPhyloseq countDominantFeatures countDominantTaxa estimateDivergence estimateDiversity estimateDominance estimateEvenness estimateFaith estimateRichness full_join getAbundanceClass getAbundant getAlpha getBestDMNFit getCCA getCluster getConditionallyLowAbundant getCrossAssociation getDissimilarity getDivergence getDMN getDominant getDPCoA getExperimentCrossAssociation getExperimentCrossCorrelation getHierarchyTree getJointRPCA getLDA getLowAbundant getMDS getMediation getNMDS getNMF getPermanentlyLowAbundant getPERMANOVA getPrevalence getPrevalent getPrevalentAbundance getPrevalentFeatures getPrevalentTaxa getRare getRareFeatures getRareTaxa getRDA getReducedDimAttribute getRPCA getTaxonomyLabels getTaxonomyRanks getTop getTopFeatures getTopTaxa getUnique getUniqueFeatures getUniqueTaxa IdTaxaToDataFrame importBIOM importHUMAnN importMetaPhlAn importMothur importQIIME2 importQZA importTaxpasta inner_join isContaminant isNotContaminant left_join loadFromBiom loadFromHumann loadFromMetaphlan loadFromMothur loadFromQIIME2 makePhyloseqFromTreeSE makePhyloseqFromTreeSummarizedExperiment makeTreeSEFromBiom makeTreeSEFromDADA2 makeTreeSEFromPhyloseq makeTreeSummarizedExperimentFromBiom makeTreeSummarizedExperimentFromDADA2 makeTreeSummarizedExperimentFromPhyloseq mapTaxonomy meltAssay meltSE mergeCols mergeFeatures mergeFeaturesByPrevalence mergeFeaturesByRank mergeRows mergeSamples mergeSEs performDMNgroupCV perSampleDominantFeatures perSampleDominantTaxa plotNMDS rarefyAssay readQZA relabundance relabundance<-relAbundanceCounts right_join runCCA runDMN runDPCoA runJSD runNMDS runOverlap runRDA runUnifrac setTaxonomyRanks splitByRanks splitOn subsampleCounts subsetByPrevalent subsetByPrevalentFeatures subsetByPrevalentTaxa subsetByRare subsetByRareFeatures subsetByRareTaxa subsetFeatures subsetSamples subsetTaxa summarizeDominance summary taxonomyRankEmpty taxonomyRanks taxonomyTree testExperimentCrossAssociation testExperimentCrossCorrelation transformAssay transformCounts transformFeatures transformSamples unsplitByRanks unsplitOn ZTransform

Dependencies:abind ape assorthead base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bluster Cairo cli cluster codetools cpp11 crayon DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial dplyr dqrng ecodive farver FNN formatR fs futile.logger futile.options generics GenomicRanges ggbeeswarm ggplot2 ggrastr ggrepel glue gridExtra gtable igraph IRanges irlba isoband jsonlite labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv MultiAssayExperiment nlme permute pheatmap pillar pkgconfig plyr png purrr R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress reshape2 rlang RSpectra rsvd Rtsne S4Arrays S4Vectors S7 ScaledMatrix scales scater scuttle Seqinfo SingleCellExperiment sitmo snow SparseArray sparseMatrixStats stringi stringr SummarizedExperiment systemfonts textshaping tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment utf8 uwot vctrs vegan vipor viridis viridisLite withr XVector yulab.utils

mia: Microbiome analysis tools

Rendered frommia.Rmdusingknitr::rmarkdown

Last update: 2025-01-16
Started: 2020-10-18

Help page	Topics
'mia' Package.	mia-package mia
Estimate alpha diversity indices	addAlpha addAlpha,SummarizedExperiment-method getAlpha getAlpha,SummarizedExperiment-method
decontam functions	addContaminantQC addContaminantQC,SummarizedExperiment-method addNotContaminantQC addNotContaminantQC,SummarizedExperiment-method isContaminant isContaminant,SummarizedExperiment-method isNotContaminant,SummarizedExperiment-method
Calculate dissimilarities	addDissimilarity addDissimilarity,SummarizedExperiment-method getDissimilarity getDissimilarity,ANY-method getDissimilarity,SummarizedExperiment-method getDissimilarity,TreeSummarizedExperiment-method
Estimate divergence	addDivergence addDivergence,SummarizedExperiment-method getDivergence getDivergence,SummarizedExperiment-method
Perform mediation analysis	addMediation addMediation,SummarizedExperiment-method getMediation getMediation,SummarizedExperiment-method
Agglomerate data based on population prevalence	agglomerateByPrevalence agglomerateByPrevalence,SummarizedExperiment-method agglomerateByPrevalence,TreeSummarizedExperiment-method
Agglomerate data using taxonomic information or other grouping	agglomerate-methods agglomerateByModule agglomerateByModule,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
Create a 'TreeSummarizedExperiment' object from 'DADA2' results	convertFromDADA2
Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results	convertFromBIOM convertToBIOM convertToBIOM,SummarizedExperiment-method importBIOM
Create a 'TreeSummarizedExperiment' object from a phyloseq object	convertFromPhyloseq convertToPhyloseq convertToPhyloseq,SummarizedExperiment-method convertToPhyloseq,TreeSummarizedExperiment-method
These functions will be deprecated. Please use other functions instead.	addPerSampleDominantFeatures addPerSampleDominantFeatures,SummarizedExperiment-method addPerSampleDominantTaxa addPerSampleDominantTaxa,SummarizedExperiment-method addTaxonomyTree addTaxonomyTree,SummarizedExperiment-method calculateJSD calculateJSD,ANY-method calculateOverlap calculateOverlap,ANY-method calculateUnifrac calculateUnifrac,ANY-method cluster cluster,SummarizedExperiment-method countDominantFeatures countDominantFeatures,SummarizedExperiment-method countDominantTaxa countDominantTaxa,SummarizedExperiment-method deprecate estimateDivergence estimateDivergence,SummarizedExperiment-method estimateDiversity estimateDiversity,ANY-method estimateDominance estimateDominance,ANY-method estimateEvenness estimateEvenness,ANY-method estimateFaith estimateFaith,ANY-method estimateRichness estimateRichness,ANY-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 makePhyloseqFromTreeSE makePhyloseqFromTreeSE,SummarizedExperiment-method makePhyloseqFromTreeSE,TreeSummarizedExperiment-method makePhyloseqFromTreeSummarizedExperiment makePhyloseqFromTreeSummarizedExperiment,ANY-method makeTreeSEFromBiom makeTreeSEFromDADA2 makeTreeSEFromPhyloseq makeTreeSummarizedExperimentFromBiom makeTreeSummarizedExperimentFromDADA2 makeTreeSummarizedExperimentFromPhyloseq makeTreeSummarizedExperimentFromPhyloseq,ANY-method 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 relabundance relabundance,SummarizedExperiment-method relabundance<- relabundance<-,SummarizedExperiment-method relAbundanceCounts relAbundanceCounts,SummarizedExperiment-method right_join right_join,ANY-method runJSD runJSD,SummarizedExperiment-method runOverlap runOverlap,SummarizedExperiment-method runUnifrac subsampleCounts subsampleCounts,SummarizedExperiment-method subsetByPrevalentFeatures subsetByPrevalentFeatures,ANY-method subsetByPrevalentTaxa subsetByPrevalentTaxa,ANY-method subsetByRareFeatures subsetByRareFeatures,ANY-method subsetByRareTaxa subsetByRareTaxa,ANY-method subsetFeatures subsetFeatures,SummarizedExperiment-method subsetSamples subsetSamples,SummarizedExperiment-method subsetTaxa subsetTaxa,SummarizedExperiment-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
Twins' microbiome data from 278 individuals	dmn_se twins
Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing	enterotype
Human esophageal community from 3 individuals	esophagus
Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.	addAbundanceClass addAbundanceClass,SingleCellExperiment-method addAbundanceClass,SummarizedExperiment-method getAbundanceClass getAbundanceClass,ANY-method getAbundanceClass,SingleCellExperiment-method getAbundanceClass,SummarizedExperiment-method getAbundant getAbundant,ANY-method getAbundant,SingleCellExperiment-method getAbundant,SummarizedExperiment-method getConditionallyLowAbundant getConditionallyLowAbundant,ANY-method getConditionallyLowAbundant,SingleCellExperiment-method getConditionallyLowAbundant,SummarizedExperiment-method getLowAbundant getLowAbundant,ANY-method getLowAbundant,SingleCellExperiment-method getLowAbundant,SummarizedExperiment-method getPermanentlyLowAbundant getPermanentlyLowAbundant,ANY-method getPermanentlyLowAbundant,SingleCellExperiment-method getPermanentlyLowAbundant,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
Clustering wrapper	addCluster addCluster,SingleCellExperiment-method addCluster,SummarizedExperiment-method getCluster getCluster,ANY-method getCluster,SingleCellExperiment-method getCluster,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
Calculation of Double Principal Correspondence analysis	addDPCoA calculateDPCoA getDPCoA getDPCoA,ANY,ANY-method getDPCoA,TreeSummarizedExperiment,missing-method runDPCoA
Calculate hierarchy tree	addHierarchyTree addHierarchyTree,SummarizedExperiment-method getHierarchyTree getHierarchyTree,SummarizedExperiment-method hierarchy-tree
Latent Dirichlet Allocation	addLDA addLDA,SummarizedExperiment-method getLDA getLDA,SummarizedExperiment-method
Perform multi-dimensional scaling (MDS)	addMDS addMDS,SingleCellExperiment-method getMDS getMDS,SingleCellExperiment-method getMDS,TreeSummarizedExperiment-method
Perform non-metric MDS on sample-level data	addNMDS calculateNMDS getNMDS getNMDS,ANY-method getNMDS,SingleCellExperiment-method getNMDS,SummarizedExperiment-method runNMDS
Non-negative Matrix Factorization	addNMF addNMF,SummarizedExperiment-method getNMF getNMF,SummarizedExperiment-method
Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)	addPERMANOVA addPERMANOVA,SummarizedExperiment-method getPERMANOVA getPERMANOVA,ANY-method getPERMANOVA,SingleCellExperiment-method getPERMANOVA,SummarizedExperiment-method
Calculation prevalence information for features across samples	addPrevalence addPrevalence,SummarizedExperiment-method addPrevalentAbundance addPrevalentAbundance,SummarizedExperiment-method 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 subsetByPrevalent,TreeSummarizedExperiment-method subsetByRare subsetByRare,SummarizedExperiment-method subsetByRare,TreeSummarizedExperiment-method
Utilization functions for 'TreeSummarizedExperiment' objects	getReducedDimAttribute getReducedDimAttribute,SingleCellExperiment-method utilization_functions
Run (joint) robust principal component analysis (RPCA)	addJointRPCA addJointRPCA,MultiAssayExperiment-method addJointRPCA,SingleCellExperiment-method addRPCA addRPCA,SummarizedExperiment-method getJointRPCA getJointRPCA,MultiAssayExperiment-method getJointRPCA,SingleCellExperiment-method getRPCA getRPCA,SingleCellExperiment-method getRPCA,SummarizedExperiment-method
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.	GlobalPatterns
Multiomics dataset from 40 rat samples	HintikkaXOData
IBDMDB 2-omic demo dataset (MGX + MTX)	ibdmdb
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
Import taxpasta-specific BIOM results to 'TreeSummarizedExperiment'	importTaxpasta
Converting a 'SummarizedExperiment' object into a long data.frame	meltSE meltSE,SingleCellExperiment-method meltSE,SummarizedExperiment-method
Merge SE objects into single SE object.	mergeSEs mergeSEs,list-method mergeSEs,SimpleList-method mergeSEs,SummarizedExperiment-method
mia datasets	mia-datasets
Skin microbial profiles 58 genetically unrelated individuals	peerj13075
Subsample Counts	rarefyAssay rarefyAssay,SummarizedExperiment-method
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
Summarizing microbiome data	getTop getTop,SummarizedExperiment-method getUnique getUnique,SummarizedExperiment-method summarizeDominance summarizeDominance,SummarizedExperiment-method summary 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
Gut microbiota profiles of 27 individuals with ADHD and healthy controls	Tengeler2020
Fecal microbiota samples from 589 patients across different colorectal cancer stages	Tito2024QMP
Transform assay	transformAssay transformAssay,SingleCellExperiment-method transformAssay,SummarizedExperiment-method

Package: mia 1.21.3

mia: Microbiome analysis

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