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Non-coding-Somatic-Mutations-in-OvCa

This repository contains custom code generated to analyze the ovarian cancer epigenome (H3K27ac ChIP-seq) and transcriptome, generate enhancer/gene maps, and identify frequently mutated regulatory elements in Ovarian Cancer using non-coding somatic single nucleotide variants (SNVs) from PCAWG.

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How to obtain genome wide enhancer-gene map

Dear authors,

I read with interest your paper in Nature Comms, congrats on your publication.
I am intrigued in your approach and have had a glance at your R scripts here. Thank you for sharing.
I am interested in trying the CREAG approach for my own study. However I have encountered a roadblock.

How do I generate the Data/enhancerGeneMapDB_spearman_genehancerHits.Rdata file, or more specifically, results/mapEnahcner2Gene_genomeWide_TADs.txt file. I presume that this is the genome wide enhancer-gene correlation file. I cannot find anywhere in your script that has been used to generate this.

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