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

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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