Package index

All functions

AnansiWeb() dimnames(<AnansiWeb>) dim(<AnansiWeb>) names(<AnansiWeb>) tableY(<AnansiWeb>) `tableY<-`(<AnansiWeb>) tableX(<AnansiWeb>) `tableX<-`(<AnansiWeb>) dictionary(<AnansiWeb>) `dictionary<-`(<AnansiWeb>) metadata(<AnansiWeb>) `metadata<-`(<AnansiWeb>) asMAE() as.list(<AnansiWeb>) as.data.frame(<AnansiWeb>) which(<AnansiWeb>) getFeaturePairs(<AnansiWeb>) mapply(<AnansiWeb>) show(<AnansiWeb>)

AnansiWeb S4 container class

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.

MultiFactor() asMultiFactor() dimnames(<MultiFactor>) dim(<MultiFactor>) names(<MultiFactor>) dictionary(<MultiFactor>) `dictionary<-`(<MultiFactor>) levels(<MultiFactor>) unfactor(<MultiFactor>) droplevels(<MultiFactor>) `[`(<MultiFactor>,<ANY>,<ANY>) `[<-`(<MultiFactor>,<ANY>,<ANY>,<list>) `[[`(<MultiFactor>,<ANY>) `[[<-`(<MultiFactor>,<ANY>,<ANY>) subset(<MultiFactor>) c(<MultiFactor>) as.list(<MultiFactor>) getEdgeList(<MultiFactor>) show(<MultiFactor>)

MultiFactor S4 container class

anansiCor()

Compute r-statistics for each featureY-featureX pair in the dictionary. Typically, the main anansi() function will run this for you.

anansiCorPvalue()

Compute r-statistics for each featureY-featureX pair in the dictionary. Typically, the main anansi() function will run this for you.

anansiCorTestByGroup()

Run correlations for all interacting metabolites and functions.

anansiDiffCor()

Run differential correlation analysis for all interacting metabolites and functions.

anansiTale-class

An S4 class to contain all anansi stats results so that they can easily be extracted.

getAnansi()

anansi wrapper for the MultiAssayExperiment class

getGraph(<MultiFactor>) getGraph(<list>)

Get a graph object out of an MultiFactor.

getWeb(<MultiAssayExperiment>)

weaveWeb wrapper for the MultiAssayExperiment class

is.categorical()

Is character, factor or ordered factor

ec2ko ec2cpd kegg_link()

Use linking data from the KEGG database.

krebs

Simplified snippet of the Krebs cycle

named_group_list()

Provide name and levels for categories for group terms

named_term_list()

Provide name and levels for categories

plotAnansi()

miaViz style plotting wrapper for anansi output

randomWeb() randomMultiFactor() krebsDemoWeb()

Generate a random AnansiWeb or MultiFactor

weaveWeb() weaveKEGG()

Weave an AnansiWeb