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

## Documentation for package ‘iNETgrate’ version 1.9.0

- 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