Search for correlation between epigenetic signals and gene expression in TADs

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Documentation for package ‘InTAD’ version 1.29.0

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

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