Annotation-Based Analysis of Specific Interactions

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Documentation for package ‘anansi’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

anansi-coercion	Coercion functions for anansi
AnansiTale	AnansiTale S7 container class. Not intended for general use.
AnansiTale-class	AnansiTale S7 container class. Not intended for general use.
AnansiWeb	AnansiWeb S7 container class
AnansiWeb-methods	Methods for AnansiWeb S7 container class
AnansiWeb-pairwise	Methods for pairwise operations on AnansiWeb objects
as.data.frame.anansi::AnansiWeb	Coercion functions for anansi
as.list.anansi::AnansiWeb	Coercion functions for anansi
as.list.anansi::MultiFactor	Coercion functions for anansi
as.MAE	Coercion functions for anansi
as.MultiAssayExperiment	Coercion functions for anansi
as.TreeSummarizedExperiment	Coercion functions for anansi
as.TSE	Coercion functions for anansi
asMAE	Coercion functions for anansi
asMultiAssayExperiment	Coercion functions for anansi
asMultiFactor	MultiFactor S7 container class
asTreeSummarizedExperiment	Coercion functions for anansi
asTSE	Coercion functions for anansi
dictionary	Get dictionary
dictionary-generic	Get dictionary
dim.anansi::AnansiWeb	Methods for AnansiWeb S7 container class
dimnames.anansi::AnansiWeb	Methods for AnansiWeb S7 container class
ec2cpd	Use linking data from the KEGG database.
ec2ko	Use linking data from the KEGG database.
FMT_KOs	Snippet of the CLR-transformed inferred functional data from the FMT Aging study.
FMT_metab	Snippet of the CLR-transformed hippocampal metabolomics data from the FMT Aging study.
FMT_metadata	Snippet of the metadata from the FMT Aging study.
getEdgeList	Get a listof edges
getFeaturePairs	Get a list of all pairs of features
getGraph	Get a graph object.
getGraph.anansi::MultiFactor	Methods for MultiFactor S7 container class
getGraph.list	Get a graph object.
kegg_link	Use linking data from the KEGG database.
krebs	Simplified snippet of the Krebs cycle
krebsDemoWeb	Generate a random AnansiWeb or MultiFactor
levels.anansi::MultiFactor	Methods for MultiFactor S7 container class
linkBiobakeryMap	make a link data.frame for biobakery mapping files input
metadata	Get metadata.
metadata-method	Get metadata.
metadata.set	Set metadata.
metadata<-	Set metadata.
metadata<--method	Set metadata.
MultiFactor	MultiFactor S7 container class
MultiFactor-methods	Methods for MultiFactor S7 container class
names.anansi::AnansiWeb	Methods for AnansiWeb S7 container class
pairs.anansi::AnansiWeb	Methods for pairwise operations on AnansiWeb objects
pairs.AnansiWeb	Methods for pairwise operations on AnansiWeb objects
pairwiseApply	Apply a function on each pair of features
pairwiseApply-generic	Apply a function on each pair of features
pairwiseApply.anansi::AnansiWeb	Methods for pairwise operations on AnansiWeb objects
pairwiseApply.AnansiWeb	Methods for pairwise operations on AnansiWeb objects
plotAnansi	Dissociation plot
plotAnansi-generic	Dissociation plot
plotAnansi-methods	Dissociation plot
randomAnansi	Generate a random AnansiWeb or MultiFactor
randomMultiFactor	Generate a random AnansiWeb or MultiFactor
randomWeb	Generate a random AnansiWeb or MultiFactor
show.anansi::AnansiWeb	Methods for AnansiWeb S7 container class
tableX	Get tableX
tableX-generic	Get tableX
tableY	Get tableY
tableY-generic	Get tableY
unfactor	Methods for MultiFactor S7 container class
unfactor-method	Methods for MultiFactor S7 container class
weaveKEGG	Weave an AnansiWeb object
weaveWeb	Weave an AnansiWeb object
weaveWeb-methods	Weave an AnansiWeb
weaveWeb.character	Weave an AnansiWeb
weaveWeb.formula	Weave an AnansiWeb
weaveWeb.MultiAssayExperiment	Weave an AnansiWeb
weaveWeb.SingleCellExperiment	Weave an AnansiWeb
weaveWeb.TreeSumarizedExperiment	Weave an AnansiWeb