Man pages for ibn-salem/chromloop
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
| addCor | Add correlation of ChIP-seq coverage to motif pairs. |
| addCovCor | Add correlation of anchor signals to pairs of close genomic... |
| addCovToGR | Add coverage to regions in 'GRanges' object. |
| addInteractionSupport | Add column to 'GInteractions' with overlap support. |
| addMotifScore | Add motif score of anchors. |
| addStrandCombination | Add combination of anchor strand orientation. |
| cutoffBest10 | Default optimal cutoff value of logistic regression. |
| cutoffByTF | Optimal cutoff values for logistic regression models. |
| getCisPairs | Build a 'GInteractions' object with all pairs of input... |
| getOutOfBound | Get out of chromosomal bound ranges. |
| modelBest10Avg | Default parameters for logistic regression model in sevenC. |
| motif.hg19.CTCF | CTCF motif locations in human genome hg19. |
| motif.hg19.CTCF.chr22 | CTCF motif locations on chromosome 22 in human genome hg19. |
| motif.hg19.CTCF.chr22.cov | CTCF motifs on human chromosome 22 with example coverage. |
| noZeroVar | returns indices of columns with non-zero variance |
| parseLoopsRao | Parse chromatin loops from Rao et al. 2014 as strict... |
| parseLoopsTang | Parse chromatin interactions from Tang et al. 2015 as... |
| predLogit | Predict interaction probability using logistic regression... |
| predLoops | Predict looping interactions. |
| prepareCisPairs | Prepares motif pairs as 'GInteractions' and add genomic... |
| sevenC | Computational chromosome conformation capture by correlation... |
| slideMean | Sliding mean over x of intervals of size k |
| TFspecificModels | TF specific parameters for logistic regression in sevenC |
