RSS-NET analysis of simulated GWAS summary statistics and B cell regulatory network
Xiang Zhu
2019-08-18
Last updated: 2020-03-06
Checks: 7 0
Knit directory: rss-net/
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Overview
Here we describe an end-to-end RSS-NET analysis of two synthetic datasets that are simulated from real genotypes of 348965 genome-wide SNPs from 1458 individuals in the UK Blood Service Control Group (Wellcome Trust Case Control Consortium, 2007) and a gene regulatory network inferred for B cells (ENCODE Project Consortium, 2012). This example gives a quick view of how RSS-NET works.
To reproduce results of this example, please use scripts in the directory wtccc_bcell/, and follow the step-by-step guide below. Before running any script in wtccc_bcell/, please install RSS-NET.
With the software installed and the input data downloaded, one should be able to run this example by simply typing the following line in shell:
If a different directory is used to store the software, input data and/or output data, please modify file paths in the given scripts accordingly.
Step-by-step illustration
Download data files
All data files required to run this example are freely available at Zenodo . Please contact me (
xiangzhu[at]stanford.edu) if you have any trouble accessing these files. After a complete download, you should see the following files.
To help readers confirm if they use the same files as we do, we report 128-bit MD5 hashes of all files in wtccc_bcell_data.md5.
To help readers confirm if they can reproduce results of this example, we also provide the results (wtccc_bcell_results.zip) in the same Zenodo deposit.
For simplicity and generality, we introduce the following short-hand notations.
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