Package index • NetCoMi

Main functions

Main functions to follow the workflow of constructing, analyzing, and comparing microbiome networks.

netConstruct(): Constructing Networks for Microbiome Data

netAnalyze(): Microbiome Network Analysis

netCompare(): Group Comparison of Network Properties

diffnet(): Constructing Differential Networks for Microbiome Data

installNetCoMiPacks(): Install all packages used within NetCoMi

Association estimation

Association estimation methods implemented in NetCoMi.

cclasso(): CCLasso: Correlation inference of Composition data through Lasso method

gcoda(): gCoda: conditional dependence network inference for compositional data

Helpers

A bunch of helpful functions that are mainly used by other functions.

createAssoPerm(): Create and store association matrices for permuted data

colToTransp(): Adding transparency to a color

calcGCD(): Graphlet Correlation Distance (GCD)

calcGCM(): Graphlet Correlation Matrix (GCM)

editLabels(): Edit labels

multAdjust(): Multiple testing adjustment

plotHeat(): Create a heatmap with p-values

renameTaxa(): Rename taxa

testGCM(): Test GCM(s) for statistical significance

S3 methods

plot(<diffnet>): Plot method for objects of class diffnet

plot(<microNetProps>): Plot Method for microNetProps Objects

print(<GCD>): Print method for GCD objects

summary(<microNetComp>) print(<summary.microNetComp>): Summary Method for Objects of Class microNetComp

summary(<microNetProps>) print(<summary.microNetProps>): Summary Method for Objects of Class microNetProps