Search for correlation between epigenetic signals and gene expression in TADs


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Documentation for package ‘InTAD’ version 1.14.0

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