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. |
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' |
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 |
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 |
filterfunSample | A sample-wise filter function builder, analogous to 'filterfun'. |
filter_taxa | Filter taxa based on abundance criteria |
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) |
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). |
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 |
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. |
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' |
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. |
rank.names | Get the names of the taxonomic ranks |
rm_outlierf | Set to FALSE any outlier species greater than f fractional abundance. |
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 | 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' |
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. |
[ | Extract parts of otuTable |
[-method | Extract parts of otuTable |