Codebase for FOCS, a new method for inferring enhancer-promoter (E-P) links and for integrative analysis of E-P links
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
R
LICENSE
README.md

README.md

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:

  1. Predicted E-P links
  2. Genomic positions of enhancers and promoters
  3. Enhancer/promoter count/RPKM profiles
  4. Sample annotations

In addition the database includes external data for integrative analysis of E-P links:

  1. ChIA-PET interactions mediated by POL2 of 4 cell types (MCF7, HCT-116, K562 and Hela-S3) taken from GSE39495
  2. 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:

  1. mkdir focs
  2. cd focs
  3. mkdir data
  4. mkdir scripts
  5. mkdir tmp

Copy the scripts in the R folder to ../focs/scripts/ folder

Additional instructions are given within tutorial.R script file