an R package for analysis, visualization and biomarker discovery of microbiome

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Documentation for package ‘MicrobiotaProcess’ version 1.2.2

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

-- A --

alphasample-class alphasample class
as.data.frame.alphasample get the table of diffAnalysisClass
as.data.frame.diffAnalysisClass get the table of diffAnalysisClass
as.treedata.taxonomyTable as.treedata

-- 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 --

clustplotClass-class clustplotClass class
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

-- 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_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.clustplotClass 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 --

import_dada2 Import function to load the feature table and taxanomy 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 --

multi_compare a container for performing two or more sample test.

-- O --

ordplotClass-class ordplotClass class

-- P --

pcasample-class pcasample class

-- R --

read_qza read the qza file, output of qiime2.

-- S --

show-method method extensions to show for diffAnalysisClass objects.
split_data Split Large Vector or DataFrame
split_str_to_list split a dataframe contained one column

-- T --

test_otu_data (Data) simulated dataset.
theme_taxbar theme_taxbar