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Example_Input
Gene_Expr
Results
VariantCalling_AWS
EPDisrupt.pl
EP_format.pl
PANGEA.pl
README.md
Run_enet.pl
cor.R
enet.R
example.sh
extractEnhMut.pl
extractGeneExpr.pl
nonc_mut.output
summary.pl

README.md

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]
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