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CoNI (version 0.1.0)

Correlation Guided Network Integration (CoNI)

Description

Integrates two numerical omics data sets from the same samples using partial correlations. The output can be represented as a network, bipartite graph or a hypergraph structure. The method used in the package refers to Klaus et al (2021) .

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Version

Install

install.packages('CoNI')

Monthly Downloads

246

Version

0.1.0

License

GPL-3

Maintainer

Jos<c3><a9> Manuel Monroy Kuhn

Last Published

September 30th, 2021

Functions in CoNI (0.1.0)

MetaboExpToy

Toy data metabolite expression
delIntFiles

Delete intermediary files
create_stackedGlobalBarplot_perTreatment

Stacked Global Barplot (One treatment)
assign_colorsAnnotation

Assing Colors to Class
barplot_VertexsPerEdgeFeature

Number Vertex features per class for every shared edge feature
chunk2

Split function
HFD_MetaboliteData

HFD metabolite data
check_previous

Check previous files
CoNIResultsHFDToy

Toy data HFD results
top_n_LF_byMagnitude

Linker Features by magnitude of effect
flattenCorrMatrix

Flatten
MetColorTable

Toy data annotation
do_objectsExist

Check if files exist
check_outputDir

Output directory
generate_network

Create network
find_localControllingFeatures

Find local controlling features
sig_correlation2Dfs

Significant correlations 2 Df
checkInputParameters

Check input parameters
sig_correlation2

Pairwise correlations
labels2colors_2

Labels to colors
createBipartiteGraph

Bipartite Network
MetaboliteAnnotation

Metabolite Annotation
getstackedGlobalBarplot_and_Grid

Stacked Global Barplot Side-by-side (two treatments)
getvertexes_edgeFeature

Get vertexes for edge feature
createBipartiteTable

Bipartite Table
split_df

Split dataset
NetStats

Network Statistics
VertexClassesSharedGenes_HFDvsChow

Toy data comparison treatments
create_edgeFBarplot

Vertex-class pairs profile of one shared edge feature
getVertexsPerEdgeFeature

Vertex Class profile per edge feature (one treatment)
getVertexsPerEdgeFeature_and_Grid

Vertex-Class profile per edge feature Side-by-Side (two treatments)
tableLCFs_VFs

Table local controlling edge features and vertex pairs
compare_sampleNames

Compare sample names
create_GlobalBarplot

Vertex-class pairs profile of shared features
countClassPerEdgeFeature

Number lipid features per class
merge_outpuSplitFiles

Merge Files.
getcolor

Get class rgb color
get_lowvarFeatures

Low variance features
obtain_groupcolors

Get colors
plotPcorvsCor

Correlation vs Partial correlation
writeTable

Write table
Compare_Triplets

Compare triplets
CoNIResults_HFD

CoNI Results HFD
Compare_VertexClasses_sharedEdgeFeatures

Table VertexClass pairs of shared Edge Features
CoNI

Correlation guided Network Integration
Chow_MetaboliteData

Chow metabolite data
Chow_GeneExpData

Chow gene expression data
CoNIResults_Chow

CoNI Results Chow
GeneExpToy

Toy data gene expression
HFD_GeneExpData

HFD gene expression data