| addCor | Adds Pearson correlation coefficient for all gene pairs |
| addGeneAnnotation | Add annotatino column of each gene to gene pairs |
| addPairDist | Add linear distance between gene paires or NA if on differnet... |
| addPairExp | Adds the expression values for both genes |
| addSameStrand | Add same starnd information. |
| addSubTADmode | Add column to indicate that two query region overlap the same... |
| addWithinSubject | Add column to indicate that query lies within at least one... |
| applyToCisPairs | Apply a function to a pair of genomic ranges. |
| applyToClosePairs | Apply a function to pairs of close genomic regions. |
| containsGenePairs | Test if gene pairs are contained in another set of gene... |
| filterForCisPairs | Get subset of gene pairs that are located on the same... |
| genepair | genepair: Functions to Analyse Pairs of Genomic Elements like... |
| getAllCisPairs | Get all possible gene pairs within a given distance range as... |
| getCor | Returns the Pearson correlation coefficient for expression of... |
| getPairAsGR | Make GRange object of range between start position of paired... |
| getPairAsGRL | Make GRangesList object of range between start position of... |
| getPairID | Creates an ID for each gene pair by concatenating both gene... |
| getPairIDsorted | Returns a unique gene ID for each pair that is independent of... |
| getRandomPairs | Sample randomly pairs from set of genes with equal... |
| interChromPairMatrix | Inter-chromosomal gene pairs counts matrix |
| nonOverlappingGenePairs | Test if gene pairs are non-overlapping. That is that two... |
| noZeroVar | returns indecies of columns with non-zero variance |
| pairNotNA | Checks that none of the genes in pairs is NA. |
| percentIncluded | Returns the percentage of gene pairs that are contained in... |
| samplePairsByWeight | Sample pairs from the input gene pairs according to given... |
| uniquePair | Remove duplicated entries of gene pairs of the form A-B and... |
| uniquePairPerGene | Get only one pair per unique gene. |
| uniquePairPerGeneBySim | Get only one pair per unique gene by choosing the gene pair... |
| weightsByBin | Compute sampling weights for continues values by binning. |
| weightsByFactorFreq | Compute sampling weights for descret values. |
