Predictive Analysis of Noncoding Genomic Alterations

Prerequisites

R packages: elasticnet, hdi

Input Files

1. Gene expression in patients.

   Format: [Patient ID]\t[FPKM]\n

2. EP pairs.

   Format: [Enh-Chr]\t[Enh-Start]\t[Enh-End]\t[Pro-Chr]\t[Pro-Position]\t[Gene]\n

3. Patient IDs.

   Format: [ID]\n

4. SNVs in patients.

   Format: [Patient ID]\t[Chr]\t[Position]\n

5. Translocation/Inversion break points.

   Format: [Patient ID]\t[BP1-Chr]\t[Position]\t[Strand]\t[BP2-Chr]\t[Position]\t[Strand]\n

6. Duplication/Deletion break points.

   Format: [Patient ID]\t[BP1-Chr]\t[Position]\t[Strand]\t[BP2-Chr]\t[Position]\t[Strand]\n

Usage

perl PANGEA.pl 
   -d [Path to PANGEA directroy]
   -n [gene name] 
   -g [gene expression] 
   -p [list of patient] 
   -e [EP pairs]
   -a [SNV]
   -b [TRAN/INV] 
   -c [CNV]