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

## Documentation for package ‘MicrobiotaProcess’ version 1.17.1

- 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