Integrates DNA methylation data with gene expression in a single gene network

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Documentation for package ‘iNETgrate’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

iNETgrate-package	Integrates DNA methylation data with gene expression in a single gene network
accelFailAnalysis	Accelerated Failure Analysis
analyzeSurvival	Survival analysis
bestInetgrator	Identifies the bestInetgrator
cleanAllData	Cleans and preprocesses data
computEigengenes	Compute eigengenes of combined modules.
computEigengloci rename	Compute eigengenes of combined modules.
computEigenloci	Computes an eigenloci for each gene
computeInetgrator	Computes an inetgrator
computeUnion	Computes union gene set
coxAnalysis	Cox analysis
createLocusGene	Mapping one locus to one gene.
distanceToTss	Computes distance of loci to the closest TSS
downloaData	Download and save TCGA data
electGenes	Selects input genes for iNETgrate analysis.
filterLowCor	Filters out genes or loci
findAliveCutoff	Find Alive Cutoff
findCore	Finds the most connected cluster of points
findTcgaDuplicates	Identify and remove duplicate samples
iNETgrate	iNETgrate - Runs entire iNETgrate pipeline.
inferEigengenes	Infers features for the test(validation) dataset
makeNetwork	Make network
plotKM	Survival (Kaplan-Meier estimator) plots
plotLociNum	Plot number of loci per gene.
plotLociTss	Plots distance of loci to genes
prepareSurvival	Prepare survival data
preprocessDnam	Cleans DNA methylation data
sample2pat	Maps sample IDs to corresponding patient IDs
sampleData	Sample Data
toyCleanedAml	A subset of cleaned TCGA-LAML data
toyComputEloci	A subset of weighted DNA methylation profile of TCGA-LAML data
toyEigengenes	A subset of weighted average of gene expression present in each module
toyRawAml	A subset of TCGA-LAML data