Package index • anansi

Package

anansi(): anansi: Annotation-based Analysis of Specific Interactions.

Methods

weaveWeb-methods weaveWeb.character weaveWeb.formula weaveWeb.MultiAssayExperiment weaveWeb.TreeSumarizedExperiment weaveWeb.SingleCellExperiment: Weave an AnansiWeb

AnansiWeb-methods show.anansi::AnansiWeb names.anansi::AnansiWeb dimnames.anansi::AnansiWeb dim.anansi::AnansiWeb: Methods for AnansiWeb S7 container class

AnansiWeb-pairwise pairs.AnansiWeb pairs.anansi::AnansiWeb pairwiseApply.AnansiWeb pairwiseApply.anansi::AnansiWeb: Methods for pairwise operations on AnansiWeb objects

MultiFactor-methods levels.anansi::MultiFactor unfactor unfactor,anansi::MultiFactor-method getGraph.anansi::MultiFactor: Methods for MultiFactor S7 container class

as.list(<anansi::AnansiWeb>) as.list(<anansi::MultiFactor>) as.data.frame(<anansi::AnansiWeb>) asMAE() asTSE(): Coercion functions for anansi

Visualisation

plotAnansi plotAnansi-generic plotAnansi-methods: Dissociation plot

Classes

AnansiWeb(): AnansiWeb S7 container class

MultiFactor(): MultiFactor S7 container class

AnansiTale(): AnansiTale S7 container class. Not intended for general use.

Generics

weaveWeb() weaveKEGG(): Weave an AnansiWeb object

pairwiseApply(): Apply a function on each pair of features

getFeaturePairs(): Get a list of all pairs of features

getEdgeList(): Get a listof edges

getGraph(): Get a graph object.

tableX(): Get tableX

tableY(): Get tableY

dictionary(): Get dictionary

metadata metadata,anansi::AnansiWeb-method: Get metadata.

metadata<- metadata.set metadata<-,anansi::AnansiWeb-method: Set metadata.

Datasets

randomWeb() randomMultiFactor() krebsDemoWeb(): Generate a random AnansiWeb or MultiFactor

FMT_data: Snippet of the CLR-transformed inferred functional data from the FMT Aging study.

FMT_data: Snippet of the CLR-transformed hippocampal metabolomics data from the FMT Aging study.

FMT_data: Snippet of the metadata from the FMT Aging study.

krebs: Simplified snippet of the Krebs cycle

ec2ko ec2cpd kegg_link(): Use linking data from the KEGG database.

Conversion utils

linkBiobakeryMap(): make a link data.frame for biobakery mapping files input