| prepareCisPairs() |
Prepares motif pairs as GInteractions and add genomic features. |
| getCisPairs() |
Build a GInteractions object with all pairs of inputGRanges within a given distance. |
| addStrandCombination() |
Add combination of anchor strand orientation. |
| addMotifScore() |
Add motif score of anchors. |
| addInteractionSupport() |
Add column to GInteractions with overlap support. |
| addCor() |
Add correlation of ChIP-seq coverage to motif pairs. |
| addCovCor() |
Add correlation of anchor signals to pairs of close genomic regions. |
| Reading genomic data |
|
| addCovToGR() |
Add coverage to regions in GRanges object. |
| parseLoopsRao() |
Parse chromatin loops from Rao et al. 2014 as strictGInteractions. |
| parseLoopsTang() |
Parse chromatin interactions from Tang et al. 2015 as GInteractions. |
| Prediction |
|
| predLoops() |
Predict looping interactions. |
| Data sets |
|
| 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. |
| modelBest10Avg |
Default parameters for logistic regression model in sevenC. |
| TFspecificModels |
TF specific parameters for logistic regression in sevenC |
| cutoffByTF |
Optimal cutoff values for logistic regression models. |
| cutoffBest10 |
Default optimal cutoff value of logistic regression. |