# sevenC
## Computational chromosome conformation capture by correlation of ChIP-seq at CTCF motifs
Chromatin looping is an important feature of
eukaryotic genomes and can bring regulatory sequences, such as enhancers or
transcription factor binding sites, in close physical proximity of regulated
target genes.
Here, we provide 7C, an R package that uses protein binding signals from ChIP-seq and
sequence motif information to predict chromatin looping events. Cross-linking
of proteins that bind close to loop anchors result in ChIP-seq signals at both
anchor loci. These signals are used at CTCF motif pairs together with their
distance and orientation to each other to predict whether they interact or not.
The resulting chromatin loops can be used to associate enhancers or
transcription factor binding sites (e.g. ChIP-seq peaks) to regulated target
genes.
## Intallation
The *sevenC* package depends on some R packages from Bioconductor. They can be
installed as follows
```R
source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer", "InteractionSet")
```
The development version can be installed from github using
devtools:
```R
#install.packages("devtools")
devtools::install_github("ibn-salem/sevenC")
```
## Basic usage example
Here we show how to use the package to predict chromatin looping interactions
among CTCF moif locations on chromosome 22.
As input only a single bigWig file is used from a STAT1 ChIP-seq experiment
in human GM12878 cells.
#### Get motif pairs
```R
library(sevenC)
# load provided CTCF motifs in human genome
motifs <- motif.hg19.CTCF.chr22
# get motifs pairs
gi <- prepareCisPairs(motifs, maxDist = 10^6)
```
#### Add ChIP-seq data and compute correaltion
```R
# use example ChIP-seq bigWig file
bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-18000000.bigWig",
package = "sevenC")
# add ChIP-seq coverage and compute correaltion at motif pairs
gi <- addCor(gi, bigWigFile)
```
#### Predict loops
```R
# predict looping interactions among all motif pairs
loops <- predLoops(gi)
```
For more detailed usage instructions, see the package
[vignette](https://ibn-salem.github.io/sevenC/articles/sevenC.html) or
[reference documentation](https://ibn-salem.github.io/sevenC/reference/index.html).
## Issues
Please report any issues here: https://github.com/ibn-salem/sevenC/issues
