PrediXcan/S-PrediXcan/S-TissueXcan Post-processing Pipeline

Introduction

• A pipeline is used to postprocess S-PrediXcan/S-TissueXcan pipeline's results

Prerequisites

• Python 3.4+
• R 3.0+
• rpy2
• annotables
• dplyr
• qqman
• ggplot2

Installation

git clone https://github.com/jiamaozheng/S-PrediXcan_Postprocessing_Pipeline

Inputs

• Prepare the following tools or files:
  • Outputs from S-PrediXcan or S-TissueXcan pipeline (required)
  • Prediction models (optional, only for analyzing S-PrediXcan output)
  • gwas_snp.txt file (tab-delimited format) prepared according to instructions and a concrete example (optional, only for generating locuszoom plots)
  • plink (optional, only for generating locuszoom plots)
• Download LocusZoom (37.5GB)(optional, only for generating locuszoom plots)

Command Line Parameters

Argument	Abbre	Required	Default	Description
--project_name	-p	Yes	None	project name (e.g ovarian_cancer)
--metaxcan_folder	-f	Yes	None	file path to metaxcan outputs
--models_folder	-d	Yes	'../data/models/'	file path to prediction models
--tools_folder	-t	No	'../data/tools/'	plink or gwas snps file
--multi_tissue	-m	No	'false'	"true" for multi_tissue
--locuszoom	-l	No	'true'	"false" for not locuszoom

Running

Example 1: To analyze outputs from S-PrediXcan pipeline

python run.py -p breast_cancer -f metaxcan_results_folder -d models_folder 

Example 2: To analyze outputs from S-PrediXcan pipeline without locuzoom plot analysis

python run.py -p breast_cancer -f metaxcan_results_folder -d models_folder -l false  

Example 3: To analyze outputs from Multi_tissue S-PrediXcan pipeline

python run.py -p breast_cancer -f metaxcan_results_folder -d models_folder -m true 

Example 4: To analyze outputs from Multi_tissue S-PrediXcan pipeline without locuzoom plot analysis

python run.py -p breast_cancer -f metaxcan_results_folder -d models_folder -m true -l false  

Outputs

• ../log/ - logs
• ../out/ - tables and figures
  • annotation .csv
  • top sigificant genes .csv
  • top sigificant genes with snps .csv
  • manhattan_plot .pdf
  • qq_plot .pdf
  • region_plot .pdf
  • bubble_plot .pdf
  • locuszoom_plot .pdf

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