| AccMatrix-class | AccMatrix class that is used to store accessibility matrices |
| compareCorCoeffs | This function returns p-values assessing the difference... |
| compareCorDistributions | This function returns p-values assessing the difference... |
| CorMatrix-class | CorMatrix class that is used to store correlation matrices |
| countReads | This function counts reads in a GRanges object that fall into... |
| cropAccMatrix | This function crops accessibility matrices |
| cropCorMatrix | This function crops correlation matrices |
| getAccLUT | This function makes a color LUT for accessibility matrices |
| getCIs | This function returns confidence intervals |
| getCorBackground | This function returns the background correlation obtained... |
| getCorLUT | This function makes a color LUT for correlation matrices |
| getCorRanges | This function returns bootstrapped correlation coefficients |
| getPEPairs | This function returns promoter-enhancer (P-E) pairs based on... |
| makeAccMatrix | This function makes accessibility matrices from a set of BED... |
| makeCorMatrix | This function makes a correlation matrix from two... |
| makeGenomeTiles | This function makes tiles for the complete hg19 genome |
| makeIPCHist | This function makes a histogram for the number of... |
| makeIPCStats | Calculate statistics for the number of integrations per cell |
| makeIPRHist | This function makes a histogram for the number of cells with... |
| makeIPRStats | Calculate statistics for the number of integrations per ROI |
| makeTiles | This function makes tiles for a particular chromosome of the... |
| PEPairs-class | PEPairs class that is used to store sets of promoter-enhancer... |
| readBed | This function reads a BED file and stores the reads in a... |
| removeEmptyRows | This function removes empty rows from accessibility matrices |
| removeRowsBelowCutoff | This function removes rows below a certain cutoff from... |
| saveImage | This function saves a matrix as an image |
| scaleAccMatrix | This function scales accessibility matrices to genomic... |
| scaleCorMatrix | This function scales correlation matrices to genomic... |
| writeMatrix | Wrapper for making and storing scaled corrleation matrices... |
