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

## Documentation for package ‘MicrobiotaProcess’ version 1.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

## -- 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.default | 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.default | 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.default | Performs a principal components analysis
get_pca.phyloseq | Performs a principal components analysis
get_pcoa | performs principal coordinate analysis (PCoA)
get_pcoa.default | 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_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.default | taxonomy barplot
ggbartax.phyloseq | 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
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.default | Rarefaction alpha index
ggrarecurve.phyloseq | 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 --

mapply_retrieve_seq | Retriveing Sequencing from NCBI By mapply
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.
retrieve_seq | Retriveing Sequencing from NCBI

## -- 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