# Handling and analysis of high-throughput phylogenetic sequence data.

## Documentation for package ‘phyloseq’ version 1.0.3

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A D E F G I M N O P R S T U misc

phyloseq-package | Handling and analysis of high-throughput phylogenetic sequence data.

## -- A --

access | Universal slot accessor function for phyloseq-class.
assign-otuTable | Assign a new OTU Table to 'x'
assign-sampleData | Assign (new) sampleData to 'x'
assign-speciesarerows | Manually change speciesAreRows through assignment.
assign-taxTab | Assign a (new) Taxonomy Table to 'x'
assign-tre | Assign a (new) phylogenetic tree to 'x'

## -- D --

data-enterotype | (Data) Enterotypes of the human gut microbiome (2011)
data-esophagus | (Data) Small example dataset from a human esophageal community (2004)
data-GlobalPatterns | (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
data-soilrep | (Data) Reproducibility of soil microbiome data (2011)
distance | General distance / dissimilarity index calculator
DPCoA | Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance

## -- E --

enterotype | (Data) Enterotypes of the human gut microbiome (2011)
esophagus | (Data) Small example dataset from a human esophageal community (2004)
estimate_richness | Summarize richness estimates
export_env_file | Export environment (ENV) file for UniFrac Server.
export_mothur_dist | Export a distance object as '.names' and '.dist' files for mothur

## -- F --

filterfunSample | A sample-wise filter function builder, analogous to 'filterfun'.
filter_taxa | Filter taxa based on abundance criteria

## -- G --

genefilterSample | Filter OTUs with arbitrary function, sample-wise.
genefilterSample-method | Filter OTUs with arbitrary function, sample-wise.
getSamples | Returns all abundance values for species 'i'.
getSamples-method | Returns all abundance values for species 'i'.
getslots.phyloseq | Return the non-empty slot names of a phyloseq object.
getSpecies | Returns all abundance values of sample 'i'.
getSpecies-method | Returns all abundance values of sample 'i'.
getTaxa | Get a unique vector of the observed taxa at a particular taxonomic rank
getVariable | Get the values for a particular variable in sampleData
GlobalPatterns | (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)

## -- I --

import | Universal import method (wrapper) for phyloseq-package
import_biom | Import phyloseq data from BIOM file
import_env_file | Read a UniFrac-formatted ENV file.
import_mothur | General function for importing mothur files into phyloseq.
import_mothur_dist | Import mothur-formatted distance file
import_pyrotagger_tab | Imports a tab-delimited version of the pyrotagger output file.
import_qiime | Import function to read files created by the QIIME pipeline.
import_RDP_cluster | Import RDP cluster file and return otuTable (abundance table).

## -- M --

make_sample_network | Make sample-wise microbiome network (igraph0)
merge_phyloseq | Merge arguments into one phyloseq object.
merge_phyloseq_pair | Merge pair of phyloseq component data objects of the same class.
merge_phyloseq_pair-method | Merge pair of phyloseq component data objects of the same class.
merge_samples | Merge samples based on a sample variable or factor.
merge_samples-method | Merge samples based on a sample variable or factor.
merge_species | Merge a subset of the species in 'x' into one species/taxa/OTU.
merge_species-method | Merge a subset of the species in 'x' into one species/taxa/OTU.
mt | Multiple testing of taxa abundance acccording to sample categories/classes
mt-method | Multiple testing of taxa abundance acccording to sample categories/classes

## -- N --

nsamples | Get the number of samples.
nsamples-method | Get the number of samples.
nspecies | Get the number of taxa/species.
nspecies-method | Get the number of taxa/species.

## -- O --

ordinate | Perform an ordination on phyloseq data
otuTable | Build or access the otuTable.
otuTable-class | The S4 class for storing taxa-abundance information.
otuTable-method | Build or access the otuTable.
otuTable<- | Assign a new OTU Table to 'x'
otuTable<--method | Assign a new OTU Table to 'x'

## -- P --

phylo-class | An S4 copy of the main phylogenetic tree class from the ape package.
phyloseq | Build phyloseq-class objects from their components.
phyloseq-class | The main experiment-level class for phyloseq data
plot_ordination | General ordination plotter based on ggplot2.
plot_phyloseq | Generic plot defaults for phyloseq.
plot_phyloseq-method | Generic plot defaults for phyloseq.
plot_richness_estimates | Plot richness estimates, flexibly with ggplot2
plot_sample_network | Plot sample-wise microbiome network (ggplot2)
plot_taxa_bar | Create a structured barplot graphic of the taxonomic groups.
plot_tree_phyloseq | Plot tree with easy tip annotation.
prune_samples | Prune unwanted samples from a phyloseq object.
prune_samples-method | Prune unwanted samples from a phyloseq object.
prune_species | Prune unwanted species / taxa from a phylogenetic object.
prune_species-method | Prune unwanted species / taxa from a phylogenetic object.

## -- R --

rank.names | Get the names of the taxonomic ranks
rm_outlierf | Set to FALSE any outlier species greater than f fractional abundance.

## -- S --

samData | Build or access sampleData.
samData<- | Assign (new) sampleData to 'x'
sample.names | Get sample names.
sample.names-method | Get sample names.
sample.variables | Get the sample variables present in sampleData
sampleData | Build or access sampleData.
sampleData-class | The S4 for storing sample variables.
sampleData-method | Build or access sampleData.
sampleData<- | Assign (new) sampleData to 'x'
sampleMap | Build or access sampleData.
sampleNames | Get sample names.
sampleSums | Returns the total number of individuals observed from each sample.
show | method extensions to show for phyloseq objects.
show-method | method extensions to show for phyloseq objects.
show_mothur_list_cutoffs | Show cutoff values available in a mothur list file
soilrep | (Data) Reproducibility of soil microbiome data (2011)
species.names | Get species / taxa names.
species.names-method | Get species / taxa names.
speciesAreRows | Access speciesAreRows slot from otuTable objects.
speciesarerows | Access speciesAreRows slot from otuTable objects.
speciesAreRows-method | Access speciesAreRows slot from otuTable objects.
speciesarerows<- | Manually change speciesAreRows through assignment.
speciesarerows<--method | Manually change speciesAreRows through assignment.
speciesSums | Returns the total number of individuals observed from each species/taxa/OTU.
subset_ord_plot | Subset points from an ordination-derived ggplot
subset_samples | Subset samples by sampleData expression
subset_species | Subset species by taxonomic expression

## -- T --

t | Transpose 'otuTable-class' or 'phyloseq-class'
t-method | Transpose 'otuTable-class' or 'phyloseq-class'
taxaplot | Create a structured barplot graphic of the taxonomic groups.
taxglom | Agglomerate taxa of the same type.
taxglom-method | Agglomerate taxa of the same type.
taxonomyTable-class | An S4 class that holds taxonomic classification data as a character matrix.
taxTab | Build or access the taxonomyTable.
taxtab | Build or access the taxonomyTable.
taxTab-method | Build or access the taxonomyTable.
taxTab<- | Assign a (new) Taxonomy Table to 'x'
threshrank | Thresholded rank transformation.
threshrankfun | A closure version of the 'threshrank' function.
tipglom | Agglomerate closely-related taxa using single-linkage clustering.
tipglom-method | Agglomerate closely-related taxa using single-linkage clustering.
tipsymbols | Annotate tips on a tree with symbols or text.
tiptext | Annotate tips on a tree with symbols or text.
topf | Make filter fun. that returns the top f fraction of taxa in a sample.
topk | Make filter fun. the most abundant 'k' taxa
topp | Make filter fun. that returns the most abundant 'p' fraction of taxa
TransformSampleCounts | Transform the abundance count data in an 'otuTable', sample-by-sample.
transformSampleCounts | Transform the abundance count data in an 'otuTable', sample-by-sample.
transformsamplecounts | Transform the abundance count data in an 'otuTable', sample-by-sample.
tre | Get phylogenetic tree from object.
tre-method | Get phylogenetic tree from object.
tre<- | Assign a (new) phylogenetic tree to 'x'
tre<--method | Assign a (new) phylogenetic tree to 'x'

## -- U --

UniFrac | Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.
UniFrac-method | Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.

## -- misc --

[ | Extract parts of otuTable
[-method | Extract parts of otuTable