FOCS
Codebase for FOCS, a new method for inferring enhancer-promoter (E-P) links and for integrative analysis of E-P links
Additional information about running FOCS can be found here
Getting FOCS database
You can download the database here. The database includes preprocessed RData files of ENCODE, Roadmap Epigenomics, FANTOM5, and GRO-seq:
- Predicted E-P links
- Genomic positions of enhancers and promoters
- Enhancer/promoter count/RPKM profiles
- Sample annotations
In addition the database includes external data for integrative analysis of E-P links:
- ChIA-PET interactions mediated by POL2 of 4 cell types (MCF7, HCT-116, K562 and Hela-S3) taken from GSE39495
- Genomic positions of GTEx eQTL data (V6 and V6p builds) taken from GTEx Portal
Dependencies
Please make sure you have the following pre-installed R packages:
- pscl
- MASS
- parallel
- AUC
- glmnet
- Matching
- RColorBrewer
- GenomicRanges
- ggplot2
Running FOCS to infer E-P links
Please note that you can run FOCS only under linux platform
First create directories:
- mkdir focs
- cd focs
- mkdir data
- mkdir scripts
- mkdir tmp
Copy the scripts in the R folder to ../focs/scripts/ folder
Additional instructions are given within tutorial.R script file