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jlim [2016/11/18 16:16]
schun created
jlim [2017/02/25 00:07] (current)
schun [Joint Likelihood Mapping (JLIM)]
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 ====== Joint Likelihood Mapping (JLIM) ====== ====== Joint Likelihood Mapping (JLIM) ======
  
-JLIM is a cross-trait test of shared causal effect, which is described in Chun et al. ([[http://biorxiv.org/content/early/2016/05/12/053165|BioRxiv]]). JLIM tests whether two traits – main and secondary – are driven by shared causal effect or not. Typically, the main trait is a large GWAS study, and secondary trait can be an expression Quantitative Trait Loci (eQTL) association study. For main trait, JLIM takes only summary-level association statistics, but for secondary trait, it requires genotype-level data to generate permutation-based null distribution.+JLIM is a cross-trait test of shared causal effect, which is described in [[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3795.html|Chun et al. 2017]]. JLIM tests whether two traits – main and secondary – are driven by shared causal effect or not. Typically, the main trait is a large GWAS study, and secondary trait can be an expression Quantitative Trait Loci (eQTL) association study. For main trait, JLIM takes only summary-level association statistics, but for secondary trait, it requires genotype-level data to generate permutation-based null distribution. ​JLIM is simultaneously released at [[https://​github.com/​cotsapaslab/​jlim|Cotsapas lab github]] and Sunyaev lab website.  
 +===== Download ===== 
 +{{ :​jlim-1.0.2.tar.gz | JLIM release v1.0.2 }}
  
 ===== How to install ===== ===== How to install =====
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 </​code>​ </​code>​
   * Generate secondary trait genotypes (.ped.gz files).   * Generate secondary trait genotypes (.ped.gz files).
-  * Generate secondary trait association and mperm files. For example, ​``` plink --bfile region1 --pheno gene1tx.pheno --linear --out LCL.gene1 --covar yourcov\\ +  * Generate secondary trait association and mperm files. For example, ​ 
---mperm 1000 --merpm-save-all --chr yourCHR --from-bp yourSTARTBP --end-bp yourENDBP+<​code>​ 
 +plink --bfile region1 --pheno gene1tx.pheno --linear --out LCL.gene1 --covar yourcov --mperm 1000 --merpm-save-all --chr yourCHR --from-bp yourSTARTBP --end-bp yourENDBP
  
 gzip LCL.gene1.assoc.linear gzip LCL.gene1.assoc.linear
  
-gzip LCL.gene1.mperm.dump.all ​``` - Run jlim_gencfg.sh and run_jlim.sh similarly as the above.+gzip LCL.gene1.mperm.dump.all 
 +</​code>​ 
 +  * Run jlim_gencfg.sh and run_jlim.sh similarly as the above.