# Search for correlation between epigenetic signals and gene expression in TADs

## Documentation for package ‘InTAD’ version 1.31.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

combineInTAD | Preparation for correlation analysis
combineWithLoops | Preparation for correlation analysis via loops
enhSel | Enhancer signals subset detected from medulloblatoma samples
enhSelGR | Genomic coordiantes of enhancer signals subet
exprs-method | Gene expression counts table
filterGeneExpr | Function to filter gene expression
findCorFromLoops | Function to perfrom correlation analysis via loops.
findCorrelation | Function to perfrom correlation analysis in TADs
fnSE | Preparation for correlation analysis for a signal
geneCoords | Gene coords GRanges
geneCoords-method | Gene coords GRanges
get.enr.bg.normfit | Function to estimate gene expression
InTADSig | The InTADSig Class
InTADSig-class | The InTADSig Class
loadSigInTAD | Load InTADSig object from text files
loopsDfSel | Data frame containing coordinates of loops
mbAnnData | Data frame containing information about samples
newSigInTAD | Create InTADSig object
plotCorAcrossRef | Function to plot correlation across genome
plotCorrelation | Function to plot correlation
rpkmCountsSel | Gene expression subset from medulloblastoma samples
sigCoords | Signal coords GRanges
sigCoords-method | Signal coords GRanges
signals | Signal values table
signals-method | Signal values table
tadGR | Genomic coordiantes of topologically associated domains
txsSel | Genomic coordiantes of genes subset