Network Construction and Comparison for Microbiome Data

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Documentation for package ‘NetCoMi’ version 1.1.0

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NetCoMi-package NetCoMi: Network Comparison for Microbial Compositional Data
.boottest Bootstrap Procedure for Testing Statistical Significance of Correlation Values
.calcAssociation Compute associations between taxa
.calcProps Calculate network properties
.getVecNames Function for Generating Vector Names
.permTestDiffAsso Permutation Tests for Determining Differential Associations
calcGCD Graphlet Correlation Distance (GCD)
calcGCM Graphlet Correlation Matrix (GCM)
cclasso CCLasso: Correlation inference of Composition data through Lasso method
colToTransp Adding transparency to a color
createAssoPerm Create and store association matrices for permuted data
diffnet Constructing Differential Networks for Microbiome Data
editLabels Edit labels
gcoda gCoda: conditional dependence network inference for compositional data
installNetCoMiPacks Install all packages used within NetCoMi
multAdjust Multiple testing adjustment
netAnalyze Microbiome Network Analysis
netCompare Group Comparison of Network Properties
netConstruct Constructing Networks for Microbiome Data
plot Plot Method for microNetProps Objects
plot.diffnet Plot method for objects of class diffnet
plot.microNetProps Plot Method for microNetProps Objects
plotHeat Create a heatmap with p-values
print.GCD Print method for GCD objects
print.summary.microNetComp Summary Method for Objects of Class microNetComp
print.summary.microNetProps Summary Method for Objects of Class microNetProps
renameTaxa Rename taxa
summary.microNetComp Summary Method for Objects of Class microNetComp
summary.microNetProps Summary Method for Objects of Class microNetProps
testGCM Test GCM(s) for statistical significance