Handling and analysis of high-throughput phylogenetic sequence data.

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Documentation for package ‘phyloseq’ version 1.0.3

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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