A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

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Documentation for package ‘MicrobiotaProcess’ version 1.14.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E G H I K M O P R S T misc

-- A --

alphasample-class	alphasample class
as.MPSE	as.MPSE method
as.mpse	as.MPSE method
as.phyloseq	convert to phyloseq object.
as.phyloseq.MPSE	convert to phyloseq object.
as.phyloseq.tbl_mpse	convert to phyloseq object.
as.treedata.taxonomyTable	as.treedata
as_phyloseq	convert to phyloseq object.

-- B --

build_tree	building tree
build_tree,character	building tree
build_tree,DNAbin	building tree
build_tree,DNAStringSet	building tree
build_tree-method	building tree

-- C --

colData<--method	MPSE accessors
convert_to_treedata	convert dataframe contained hierarchical relationship or other classes to treedata class

-- D --

data-hmp_aerobiosis_small	(Data) Small subset of the HMP 16S dataset
data-kostic2012crc	(Data) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma (2012)
data-test_otu_data	(Data) simulated dataset.
diffAnalysisClass-class	diffAnalysisClass class
diff_analysis	Differential expression analysis
diff_analysis.data.frame	Differential expression analysis
diff_analysis.phyloseq	Differential expression analysis
drop_taxa	Dropping Species with Few abundance and Few Occurrences
drop_taxa,data.frame	Dropping Species with Few abundance and Few Occurrences
drop_taxa,phyloseq	Dropping Species with Few abundance and Few Occurrences
drop_taxa-method	Dropping Species with Few abundance and Few Occurrences
dr_extract	Extracting the internal tbl_df attribute of tibble.

-- E --

extract_binary_offspring

extract the binary offspring of the specified internal nodes

-- G --

generalizedFC	generalized fold change
generalizedFC.default	generalized fold change
generalizedFC.formula	generalized fold change
get_alphaindex	alpha index
get_alphaindex,data.frame	alpha index
get_alphaindex,integer	alpha index
get_alphaindex,matrix	alpha index
get_alphaindex,numeric	alpha index
get_alphaindex,phyloseq	alpha index
get_alphaindex-method	alpha index
get_clust	Hierarchical cluster analysis for the samples
get_clust.data.frame	Hierarchical cluster analysis for the samples
get_clust.dist	Hierarchical cluster analysis for the samples
get_clust.phyloseq	Hierarchical cluster analysis for the samples
get_coord	get ordination coordinates.
get_coord.pcoa	get ordination coordinates.
get_coord.prcomp	get ordination coordinates.
get_count	calculate the count or relative abundance of replicate element with a speficify column
get_dist	calculate distance
get_dist.data.frame	calculate distance
get_dist.phyloseq	calculate distance
get_mean_median	get the mean and median of specific feature.
get_NRI_NTI	calculating related phylogenetic alpha metric
get_NRI_NTI,data.frame	calculating related phylogenetic alpha metric
get_NRI_NTI,matrix	calculating related phylogenetic alpha metric
get_NRI_NTI,phyloseq	calculating related phylogenetic alpha metric
get_NRI_NTI-method	calculating related phylogenetic alpha metric
get_pca	Performs a principal components analysis
get_pca.data.frame	Performs a principal components analysis
get_pca.phyloseq	Performs a principal components analysis
get_pcoa	performs principal coordinate analysis (PCoA)
get_pcoa.data.frame	performs principal coordinate analysis (PCoA)
get_pcoa.dist	performs principal coordinate analysis (PCoA)
get_pcoa.phyloseq	performs principal coordinate analysis (PCoA)
get_pvalue	Methods for computation of the p-value
get_pvalue.glm	Methods for computation of the p-value
get_pvalue.htest	Methods for computation of the p-value
get_pvalue.lm	Methods for computation of the p-value
get_pvalue.lme	Methods for computation of the p-value
get_pvalue.negbin	Methods for computation of the p-value
get_pvalue.QuadTypeIndependenceTest	Methods for computation of the p-value
get_pvalue.ScalarIndependenceTest	Methods for computation of the p-value
get_rarecurve	obtain the result of rare curve
get_rarecurve,data.frame	obtain the result of rare curve
get_rarecurve,phyloseq	obtain the result of rare curve
get_rarecurve-method	obtain the result of rare curve
get_ratio	calculate the count or relative abundance of replicate element with a speficify column
get_sampledflist	Generate random data list from a original data.
get_taxadf	get the data of specified taxonomy
get_taxadf,data.frame	get the data of specified taxonomy
get_taxadf,phyloseq	get the data of specified taxonomy
get_taxadf-method	get the data of specified taxonomy
get_upset	generate the dataset for upset of UpSetR
get_upset,data.frame	generate the dataset for upset of UpSetR
get_upset,phyloseq	generate the dataset for upset of UpSetR
get_upset-method	generate the dataset for upset of UpSetR
get_varct	get the contribution of variables
get_varct.pcasample	get the contribution of variables
get_varct.pcoa	get the contribution of variables
get_varct.prcomp	get the contribution of variables
get_vennlist	generate a vennlist for VennDiagram
get_vennlist,data.framet	generate a vennlist for VennDiagram
get_vennlist,phyloseq	generate a vennlist for VennDiagram
get_vennlist-method	generate a vennlist for VennDiagram
ggbartax	taxonomy barplot
ggbartax.data.frame	taxonomy barplot
ggbartax.phyloseq	taxonomy barplot
ggbartaxa	taxonomy barplot
ggbox	A box or violin plot with significance test
ggbox,alphasample	A box or violin plot with significance test
ggbox,data.frame	A box or violin plot with significance test
ggbox-method	A box or violin plot with significance test
ggclust	plot the result of hierarchical cluster analysis for the samples
ggclust.treedata	plot the result of hierarchical cluster analysis for the samples
ggdiffbartaxa	significantly discriminative feature barplot
ggdiffbox	boxplot for the result of diff_analysis
ggdiffbox,diffAnalysisClass	boxplot for the result of diff_analysis
ggdiffbox-method	boxplot for the result of diff_analysis
ggdiffclade	plot the clade tree with highlight
ggdiffclade.data.frame	plot the clade tree with highlight
ggdiffclade.diffAnalysisClass	plot the clade tree with highlight
ggdifftaxbar	significantly discriminative feature barplot
ggdifftaxbar,diffAnalysisClass	significantly discriminative feature barplot
ggdifftaxbar-method	significantly discriminative feature barplot
ggdifftaxbar.featureMeanMedian	significantly discriminative feature barplot
ggeffectsize	visualization of effect size by the Linear Discriminant Analysis or randomForest
ggeffectsize.data.frame	visualization of effect size by the Linear Discriminant Analysis or randomForest
ggeffectsize.diffAnalysisClass	visualization of effect size by the Linear Discriminant Analysis or randomForest
ggordpoint	ordination plotter based on ggplot2.
ggordpoint.default	ordination plotter based on ggplot2.
ggordpoint.pcasample	ordination plotter based on ggplot2.
ggrarecurve	Rarefaction alpha index
ggrarecurve.data.frame	Rarefaction alpha index
ggrarecurve.phyloseq	Rarefaction alpha index
ggrarecurve.rarecurve	Rarefaction alpha index

-- H --

hmp_aerobiosis_small

(Data) Small subset of the HMP 16S dataset

-- I --

ImportDada2	Import function to load the feature table and taxonomy table of dada2
ImportQiime2	Import function to load the output of qiime2.
import_dada2	Import function to load the feature table and taxonomy table of dada2
import_qiime2	Import function to load the output of qiime2.

-- K --

kostic2012crc

(Data) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma (2012)

-- M --

mouse.time.mpse	(Data) An example data
MPSE	Construct a MPSE object
MPSE-accessors	MPSE accessors
MPSE-class	MPSE class
mp_adonis	Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object
mp_adonis,grouped_df_mpse	Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object
mp_adonis,MPSE	Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object
mp_adonis,tbl_mpse	Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object
mp_adonis-method	Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object
mp_aggregate	aggregate the assays with the specific group of sample and fun.
mp_aggregate,MPSE	aggregate the assays with the specific group of sample and fun.
mp_aggregate-method	aggregate the assays with the specific group of sample and fun.
mp_aggregate_clade	calculate the mean/median (relative) abundance of internal nodes according to their children tips.
mp_aggregate_clade,grouped_df_mpse	calculate the mean/median (relative) abundance of internal nodes according to their children tips.
mp_aggregate_clade,MPSE	calculate the mean/median (relative) abundance of internal nodes according to their children tips.
mp_aggregate_clade,tbl_mpse	calculate the mean/median (relative) abundance of internal nodes according to their children tips.
mp_aggregate_clade-method	calculate the mean/median (relative) abundance of internal nodes according to their children tips.
mp_anosim	Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object
mp_anosim,grouped_df_mpse	Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object
mp_anosim,MPSE	Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object
mp_anosim,tbl_mpse	Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object
mp_anosim-method	Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse object
mp_balance_clade	Calculating the balance score of internal nodes (clade) according to the geometric.mean/mean/median abundance of their binary children tips.
mp_balance_clade,grouped_df_mpse	Calculating the balance score of internal nodes (clade) according to the geometric.mean/mean/median abundance of their binary children tips.
mp_balance_clade,MPSE	Calculating the balance score of internal nodes (clade) according to the geometric.mean/mean/median abundance of their binary children tips.
mp_balance_clade,tbl_mpse	Calculating the balance score of internal nodes (clade) according to the geometric.mean/mean/median abundance of their binary children tips.
mp_balance_clade-method	Calculating the balance score of internal nodes (clade) according to the geometric.mean/mean/median abundance of their binary children tips.
mp_cal_abundance	Calculate the (relative) abundance of each taxonomy class for each sample or group.
mp_cal_abundance,grouped_df_mpse	Calculate the (relative) abundance of each taxonomy class for each sample or group.
mp_cal_abundance,MPSE	Calculate the (relative) abundance of each taxonomy class for each sample or group.
mp_cal_abundance,tbl_mpse	Calculate the (relative) abundance of each taxonomy class for each sample or group.
mp_cal_abundance-method	Calculate the (relative) abundance of each taxonomy class for each sample or group.
mp_cal_alpha	calculate the alpha index with MPSE or tbl_mpse
mp_cal_alpha,grouped_df_mpse	calculate the alpha index with MPSE or tbl_mpse
mp_cal_alpha,MPSE	calculate the alpha index with MPSE or tbl_mpse
mp_cal_alpha,tbl_mpse	calculate the alpha index with MPSE or tbl_mpse
mp_cal_alpha-method	calculate the alpha index with MPSE or tbl_mpse
mp_cal_cca	[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_cca,grouped_df_mpse	[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_cca,MPSE	[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_cca,tbl_mpse	[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_cca-method	[Partial] [Constrained] Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_clust	Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object
mp_cal_clust,grouped_df_mpse	Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object
mp_cal_clust,MPSE	Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object
mp_cal_clust,tbl_mpse	Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object
mp_cal_clust-method	Hierarchical cluster analysis for the samples with MPSE or tbl_mpse object
mp_cal_dca	Detrended Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_dca,grouped_df_mpse	Detrended Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_dca,MPSE	Detrended Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_dca,tbl_mpse	Detrended Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_dca-method	Detrended Correspondence Analysis with MPSE or tbl_mpse object
mp_cal_dist	Calculate the distances between the samples or features with specified abundance.
mp_cal_dist,grouped_df_mpse	Calculate the distances between the samples or features with specified abundance.
mp_cal_dist,MPSE	Calculate the distances between the samples or features with specified abundance.
mp_cal_dist,tbl_mpse	Calculate the distances between the samples or features with specified abundance.
mp_cal_dist-method	Calculate the distances between the samples or features with specified abundance.
mp_cal_divergence	calculate the divergence with MPSE or tbl_mpse
mp_cal_divergence,grouped_df_mpse	calculate the divergence with MPSE or tbl_mpse
mp_cal_divergence,MPSE	calculate the divergence with MPSE or tbl_mpse
mp_cal_divergence,tbl_mpse	calculate the divergence with MPSE or tbl_mpse
mp_cal_divergence-method	calculate the divergence with MPSE or tbl_mpse
mp_cal_nmds	Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object
mp_cal_nmds,grouped_df_mpse	Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object
mp_cal_nmds,MPSE	Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object
mp_cal_nmds,tbl_mpse	Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object
mp_cal_nmds-method	Nonmetric Multidimensional Scaling Analysis with MPSE or tbl_mpse object
mp_cal_pca	Principal Components Analysis with MPSE or tbl_mpse object
mp_cal_pca,grouped_df_mpse	Principal Components Analysis with MPSE or tbl_mpse object
mp_cal_pca,MPSE	Principal Components Analysis with MPSE or tbl_mpse object
mp_cal_pca,tbl_mpse	Principal Components Analysis with MPSE or tbl_mpse object
mp_cal_pca-method	Principal Components Analysis with MPSE or tbl_mpse object
mp_cal_pcoa	Principal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pcoa,grouped_df_mpse	Principal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pcoa,MPSE	Principal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pcoa,tbl_mpse	Principal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pcoa-method	Principal Coordinate Analysis with MPSE or tbl_mpse object
mp_cal_pd_metric	Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object
mp_cal_pd_metric,grouped_df_mpse	Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object
mp_cal_pd_metric,MPSE	Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object
mp_cal_pd_metric,tbl_mpse	Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object
mp_cal_pd_metric-method	Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object
mp_cal_rarecurve	Calculating the different alpha diversities index with different depth
mp_cal_rarecurve,grouped_df_mpse	Calculating the different alpha diversities index with different depth
mp_cal_rarecurve,MPSE	Calculating the different alpha diversities index with different depth
mp_cal_rarecurve,tbl_mpse	Calculating the different alpha diversities index with different depth
mp_cal_rarecurve-method	Calculating the different alpha diversities index with different depth
mp_cal_rda	[Partial] [Constrained] Redundancy Analysis with MPSE or tbl_mpse object
mp_cal_rda,grouped_df_mpse	[Partial] [Constrained] Redundancy Analysis with MPSE or tbl_mpse object
mp_cal_rda,MPSE	[Partial] [Constrained] Redundancy Analysis with MPSE or tbl_mpse object
mp_cal_rda,tbl_mpse	[Partial] [Constrained] Redundancy Analysis with MPSE or tbl_mpse object
mp_cal_rda-method	[Partial] [Constrained] Redundancy Analysis with MPSE or tbl_mpse object
mp_cal_upset	Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'
mp_cal_upset,grouped_df_mpse	Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'
mp_cal_upset,MPSE	Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'
mp_cal_upset,tbl_mpse	Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'
mp_cal_upset-method	Calculating the samples or groups for each OTU, the result can be visualized by 'ggupset'
mp_cal_venn	Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'
mp_cal_venn,grouped_df_mpse	Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'
mp_cal_venn,MPSE	Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'
mp_cal_venn,tbl_mpse	Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'
mp_cal_venn-method	Calculating the OTU for each sample or group, the result can be visualized by 'ggVennDiagram'
mp_decostand	This Function Provideds Several Standardization Methods for Community Data
mp_decostand,data.frame	This Function Provideds Several Standardization Methods for Community Data
mp_decostand,grouped_df_mpse	This Function Provideds Several Standardization Methods for Community Data
mp_decostand,MPSE	This Function Provideds Several Standardization Methods for Community Data
mp_decostand,tbl_mpse	This Function Provideds Several Standardization Methods for Community Data
mp_decostand-method	This Function Provideds Several Standardization Methods for Community Data
mp_diff_analysis	Differential expression analysis for MPSE or tbl_mpse object
mp_diff_analysis,grouped_df_mpse	Differential expression analysis for MPSE or tbl_mpse object
mp_diff_analysis,MPSE	Differential expression analysis for MPSE or tbl_mpse object
mp_diff_analysis,tbl_mpse	Differential expression analysis for MPSE or tbl_mpse object
mp_diff_analysis-method	Differential expression analysis for MPSE or tbl_mpse object
mp_diff_clade	Differential internal and tip nodes (clades) analysis for MPSE or tbl_mpse object
mp_diff_clade,grouped_df_mpse	Differential internal and tip nodes (clades) analysis for MPSE or tbl_mpse object
mp_diff_clade,MPSE	Differential internal and tip nodes (clades) analysis for MPSE or tbl_mpse object
mp_diff_clade,tbl_mpse	Differential internal and tip nodes (clades) analysis for MPSE or tbl_mpse object
mp_diff_clade-method	Differential internal and tip nodes (clades) analysis for MPSE or tbl_mpse object
mp_dmn	Fit Dirichlet-Multinomial models to MPSE or tbl_mpse
mp_dmn,grouped_df_mpse	Fit Dirichlet-Multinomial models to MPSE or tbl_mpse
mp_dmn,MPSE	Fit Dirichlet-Multinomial models to MPSE or tbl_mpse
mp_dmn,tbl_mpse	Fit Dirichlet-Multinomial models to MPSE or tbl_mpse
mp_dmn-method	Fit Dirichlet-Multinomial models to MPSE or tbl_mpse
mp_dmngroup	Dirichlet-Multinomial generative classifiers to MPSE or tbl_mpse
mp_dmngroup,grouped_df_mpse	Dirichlet-Multinomial generative classifiers to MPSE or tbl_mpse
mp_dmngroup,MPSE	Dirichlet-Multinomial generative classifiers to MPSE or tbl_mpse
mp_dmngroup,tbl_mpse	Dirichlet-Multinomial generative classifiers to MPSE or tbl_mpse
mp_dmngroup-method	Dirichlet-Multinomial generative classifiers to MPSE or tbl_mpse
mp_envfit	Fits an Environmental Vector or Factor onto an Ordination With MPSE or tbl_mpse Object
mp_envfit,grouped_df_mpse	Fits an Environmental Vector or Factor onto an Ordination With MPSE or tbl_mpse Object
mp_envfit,MPSE	Fits an Environmental Vector or Factor onto an Ordination With MPSE or tbl_mpse Object
mp_envfit,tbl_mpse	Fits an Environmental Vector or Factor onto an Ordination With MPSE or tbl_mpse Object
mp_envfit-method	Fits an Environmental Vector or Factor onto an Ordination With MPSE or tbl_mpse Object
mp_extract_abundance	Extracting the abundance metric from MPSE or tbl_mpse object
mp_extract_abundance,grouped_df_mpse	Extracting the abundance metric from MPSE or tbl_mpse object
mp_extract_abundance,MPSE	Extracting the abundance metric from MPSE or tbl_mpse object
mp_extract_abundance,tbl_mpse	Extracting the abundance metric from MPSE or tbl_mpse object
mp_extract_abundance-method	Extracting the abundance metric from MPSE or tbl_mpse object
mp_extract_assays	extract the abundance matrix from MPSE object or tbl_mpse object
mp_extract_assays,grouped_df_mpse	extract the abundance matrix from MPSE object or tbl_mpse object
mp_extract_assays,MPSE	extract the abundance matrix from MPSE object or tbl_mpse object
mp_extract_assays,tbl_mpse	extract the abundance matrix from MPSE object or tbl_mpse object
mp_extract_assays-method	extract the abundance matrix from MPSE object or tbl_mpse object
mp_extract_dist	extract the dist object from MPSE or tbl_mpse object
mp_extract_dist,grouped_df_mpse	extract the dist object from MPSE or tbl_mpse object
mp_extract_dist,MPSE	extract the dist object from MPSE or tbl_mpse object
mp_extract_dist,tbl_mpse	extract the dist object from MPSE or tbl_mpse object
mp_extract_dist-method	extract the dist object from MPSE or tbl_mpse object
mp_extract_feature	extract the feature (OTU) information in MPSE object
mp_extract_feature,grouped_df_mpse	extract the feature (OTU) information in MPSE object
mp_extract_feature,MPSE	extract the feature (OTU) information in MPSE object
mp_extract_feature,tbl_mpse	extract the feature (OTU) information in MPSE object
mp_extract_feature-method	extract the feature (OTU) information in MPSE object
mp_extract_internal_attr	Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse object
mp_extract_internal_attr,grouped_df_mpse	Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse object
mp_extract_internal_attr,MPSE	Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse object
mp_extract_internal_attr,tbl_mpse	Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse object
mp_extract_internal_attr-method	Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse object
mp_extract_otutree	extract the taxonomy tree in MPSE object
mp_extract_rarecurve	Extract the result of mp_cal_rarecurve with action="add" from MPSE or tbl_mpse object
mp_extract_rarecurve,grouped_df_mpse	Extract the result of mp_cal_rarecurve with action="add" from MPSE or tbl_mpse object
mp_extract_rarecurve,MPSE	Extract the result of mp_cal_rarecurve with action="add" from MPSE or tbl_mpse object
mp_extract_rarecurve,tbl_mpse	Extract the result of mp_cal_rarecurve with action="add" from MPSE or tbl_mpse object
mp_extract_rarecurve-method	Extract the result of mp_cal_rarecurve with action="add" from MPSE or tbl_mpse object
mp_extract_refseq	Extract the representative sequences from MPSE object
mp_extract_refseq,grouped_df_mpse	Extract the representative sequences from MPSE object
mp_extract_refseq,MPSE	Extract the representative sequences from MPSE object
mp_extract_refseq,tbl_mpse	Extract the representative sequences from MPSE object
mp_extract_refseq-method	Extract the representative sequences from MPSE object
mp_extract_sample	extract the sample information in MPSE object
mp_extract_sample,grouped_df_mpse	extract the sample information in MPSE object
mp_extract_sample,MPSE	extract the sample information in MPSE object
mp_extract_sample,tbl_mpse	extract the sample information in MPSE object
mp_extract_sample-method	extract the sample information in MPSE object
mp_extract_taxatree	extract the taxonomy tree in MPSE object
mp_extract_taxonomy	extract the taxonomy annotation in MPSE object
mp_extract_taxonomy,grouped_df_mpse	extract the taxonomy annotation in MPSE object
mp_extract_taxonomy,MPSE	extract the taxonomy annotation in MPSE object
mp_extract_taxonomy,tbl_mpse	extract the taxonomy annotation in MPSE object
mp_extract_taxonomy-method	extract the taxonomy annotation in MPSE object
mp_extract_tree	extract the taxonomy tree in MPSE object
mp_extract_tree,grouped_df_mpse	extract the taxonomy tree in MPSE object
mp_extract_tree,MPSE	extract the taxonomy tree in MPSE object
mp_extract_tree,tbl_mpse	extract the taxonomy tree in MPSE object
mp_extract_tree-method	extract the taxonomy tree in MPSE object
mp_filter_taxa	Filter OTU (Features) By Abundance Level
mp_filter_taxa,grouped_df_mpse	Filter OTU (Features) By Abundance Level
mp_filter_taxa,MPSE	Filter OTU (Features) By Abundance Level
mp_filter_taxa,tbl_mpse	Filter OTU (Features) By Abundance Level
mp_filter_taxa-method	Filter OTU (Features) By Abundance Level
mp_fortify	mp_fortify
mp_import_biom	building MPSE object from biom-format file.
mp_import_dada2	Import function to load the feature table and taxonomy table of dada2
mp_import_humann_regroup	Import function to load the output of human_regroup_table in HUMAnN.
mp_import_metaphlan	Import function to load the output of MetaPhlAn.
mp_import_qiime	Import function to load the output of qiime.
mp_import_qiime2	Import function to load the output of qiime2.
mp_mantel	Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object
mp_mantel,grouped_df_mpse	Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object
mp_mantel,MPSE	Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object
mp_mantel,tbl_mpse	Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object
mp_mantel-method	Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object
mp_mrpp	Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object
mp_mrpp,grouped_df_mpse	Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object
mp_mrpp,MPSE	Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object
mp_mrpp,tbl_mpse	Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object
mp_mrpp-method	Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object
mp_plot_abundance	plotting the abundance of taxa via specified taxonomy class
mp_plot_abundance,grouped_df_mpse	plotting the abundance of taxa via specified taxonomy class
mp_plot_abundance,MPSE	plotting the abundance of taxa via specified taxonomy class
mp_plot_abundance,tbl_mpse	plotting the abundance of taxa via specified taxonomy class
mp_plot_abundance-method	plotting the abundance of taxa via specified taxonomy class
mp_plot_alpha	Plotting the alpha diversity between samples or groups.
mp_plot_alpha,grouped_df_mpse	Plotting the alpha diversity between samples or groups.
mp_plot_alpha,MPSE	Plotting the alpha diversity between samples or groups.
mp_plot_alpha,tbl_mpse	Plotting the alpha diversity between samples or groups.
mp_plot_alpha-method	Plotting the alpha diversity between samples or groups.
mp_plot_diff_boxplot	displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).
mp_plot_diff_boxplot,grouped_df_mpse	displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).
mp_plot_diff_boxplot,MPSE	displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).
mp_plot_diff_boxplot,tbl_mpse	displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).
mp_plot_diff_boxplot-method	displaying the differential result contained abundance and LDA with boxplot (abundance) and error bar (LDA).
mp_plot_diff_cladogram	Visualizing the result of mp_diff_analysis with cladogram.
mp_plot_diff_manhattan	displaying the differential result contained abundance and LDA with manhattan plot.
mp_plot_diff_manhattan,grouped_df_mpse	displaying the differential result contained abundance and LDA with manhattan plot.
mp_plot_diff_manhattan,MPSE	displaying the differential result contained abundance and LDA with manhattan plot.
mp_plot_diff_manhattan,tbl_mpse	displaying the differential result contained abundance and LDA with manhattan plot.
mp_plot_diff_manhattan-method	displaying the differential result contained abundance and LDA with manhattan plot.
mp_plot_diff_res	The visualization of result of mp_diff_analysis
mp_plot_diff_res,grouped_df_mpse	The visualization of result of mp_diff_analysis
mp_plot_diff_res,MPSE	The visualization of result of mp_diff_analysis
mp_plot_diff_res,tbl_mpse	The visualization of result of mp_diff_analysis
mp_plot_diff_res-method	The visualization of result of mp_diff_analysis
mp_plot_dist	Plotting the distance between the samples with heatmap or boxplot.
mp_plot_dist,grouped_df_mpse	Plotting the distance between the samples with heatmap or boxplot.
mp_plot_dist,MPSE	Plotting the distance between the samples with heatmap or boxplot.
mp_plot_dist,tbl_mpse	Plotting the distance between the samples with heatmap or boxplot.
mp_plot_dist-method	Plotting the distance between the samples with heatmap or boxplot.
mp_plot_ord	Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA
mp_plot_ord,grouped_df_mpse	Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA
mp_plot_ord,MPSE	Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA
mp_plot_ord,tbl_mpse	Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA
mp_plot_ord-method	Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA
mp_plot_rarecurve	Rarefaction alpha index with MPSE
mp_plot_rarecurve,grouped_tbl_mpse	Rarefaction alpha index with MPSE
mp_plot_rarecurve,MPSE	Rarefaction alpha index with MPSE
mp_plot_rarecurve,tbl_mpse	Rarefaction alpha index with MPSE
mp_plot_rarecurve-method	Rarefaction alpha index with MPSE
mp_plot_upset	Plotting the different number of OTU between group via UpSet plot
mp_plot_upset,grouped_df_mpse	Plotting the different number of OTU between group via UpSet plot
mp_plot_upset,MPSE	Plotting the different number of OTU between group via UpSet plot
mp_plot_upset,tbl_mpse	Plotting the different number of OTU between group via UpSet plot
mp_plot_upset-method	Plotting the different number of OTU between group via UpSet plot
mp_plot_venn	Plotting the different number of OTU between groups with Venn Diagram.
mp_plot_venn,grouped_df_mpse	Plotting the different number of OTU between groups with Venn Diagram.
mp_plot_venn,MPSE	Plotting the different number of OTU between groups with Venn Diagram.
mp_plot_venn,tbl_mpse	Plotting the different number of OTU between groups with Venn Diagram.
mp_plot_venn-method	Plotting the different number of OTU between groups with Venn Diagram.
mp_rrarefy	mp_rrarefy method
mp_rrarefy,grouped_df_mpse	mp_rrarefy method
mp_rrarefy,MPSE	mp_rrarefy method
mp_rrarefy,tbl_mpse	mp_rrarefy method
mp_rrarefy-method	mp_rrarefy method
mp_select_as_tip	select specific taxa level as rownames of MPSE
mp_select_as_tip,grouped_df_mpse	select specific taxa level as rownames of MPSE
mp_select_as_tip,MPSE	select specific taxa level as rownames of MPSE
mp_select_as_tip,tbl_mpse	select specific taxa level as rownames of MPSE
mp_select_as_tip-method	select specific taxa level as rownames of MPSE
mp_stat_taxa	Count the number and total number taxa for each sample at different taxonomy levels
mp_stat_taxa,grouped_df_mpse	Count the number and total number taxa for each sample at different taxonomy levels
mp_stat_taxa,MPSE	Count the number and total number taxa for each sample at different taxonomy levels
mp_stat_taxa,tbl_mpse	Count the number and total number taxa for each sample at different taxonomy levels
mp_stat_taxa-method	Count the number and total number taxa for each sample at different taxonomy levels
multi_compare	a container for performing two or more sample test.

-- O --

ordplotClass-class	ordplotClass class
otutree	MPSE accessors
otutree,group_df_mpse	MPSE accessors
otutree,MPSE	MPSE accessors
otutree,tbl_mpse	MPSE accessors
otutree-method	MPSE accessors
otutree<-	MPSE accessors
otutree<-,grouped_df_mpse	MPSE accessors
otutree<-,MPSE	MPSE accessors
otutree<-,tbl_mpse	MPSE accessors
otutree<--method	MPSE accessors

-- P --

pcasample-class	pcasample class
print	print some objects
print.grouped_df_mpse	print some objects
print.MPSE	print some objects
print.rarecurve	print some objects
print.tbl_mpse	print some objects

-- R --

read_qza	read the qza file, output of qiime2.
refsequence	MPSE accessors
refsequence,MPSE	MPSE accessors
refsequence-method	MPSE accessors
refsequence<-	MPSE accessors
refsequence<-,MPSE	MPSE accessors
refsequence<--method	MPSE accessors
rownames<-,MPSE	MPSE accessors
rownames<--method	MPSE accessors

-- S --

scale_fill_diff_cladogram	Create the scale of mp_plot_diff_cladogram.
set_diff_boxplot_color	set the color scale of plot generated by mp_plot_diff_boxplot
set_scale_theme	adjust the color of heatmap of mp_plot_dist
show-method	method extensions to show for diffAnalysisClass or alphasample objects.
split_data	Split Large Vector or DataFrame
split_str_to_list	split a dataframe contained one column

-- T --

taxatree	MPSE accessors
taxatree,grouped_df_mpse	MPSE accessors
taxatree,MPSE	MPSE accessors
taxatree,tbl_mpse	MPSE accessors
taxatree-method	MPSE accessors
taxatree<-	MPSE accessors
taxatree<-,grouped_df_mpse	MPSE accessors
taxatree<-,MPSE	MPSE accessors
taxatree<-,tbl_mpse	MPSE accessors
taxatree<--method	MPSE accessors
taxonomy	extract the taxonomy annotation in MPSE object
taxonomy,grouped_df_mpse	extract the taxonomy annotation in MPSE object
taxonomy,MPSE	extract the taxonomy annotation in MPSE object
taxonomy,tbl_mpse	extract the taxonomy annotation in MPSE object
taxonomy-method	extract the taxonomy annotation in MPSE object
taxonomy<-	MPSE accessors
taxonomy<-,MPSE	MPSE accessors
taxonomy<--method	MPSE accessors
tax_table	MPSE accessors
tax_table,grouped_df_mpse	MPSE accessors
tax_table,MPSE	MPSE accessors
tax_table,tbl_mpse	MPSE accessors
tax_table-method	MPSE accessors
test_otu_data	(Data) simulated dataset.
theme_taxbar	theme_taxbar

-- misc --

[-method

MPSE accessors