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jlim2.0 [2019/12/06 14:25] – created - external edit 127.0.0.1jlim2.0 [2023/01/20 10:04] (current) – [JLIM 2.0] schun
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 ====== JLIM 2.0 ====== ====== JLIM 2.0 ======
  
-Has the added functionality of obtaining association statistics for the secondary trait in a cohort specific manner and then combining them before running JLIM. It is designed for meta-analyses of secondary trait cohorts with matching ancestries. JLIM 2.0 is described in (https://www.biorxiv.org/content/10.1101/832162v1) +Has the added functionality of obtaining association statistics for the secondary trait in a cohort specific manner and then combining them before running JLIM. It is designed for meta-analyses of secondary trait cohorts with matching ancestries. JLIM 2.0 is described in [[https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010557|Chun & Akle et al. 2022]].
  
 ===== Download ===== ===== Download =====
 Code Code
  
-{{ :jlim_2.0_ne.tar.gz | JLIM release v2 }}+  * {{ :jlim_2.0_ne.tar.gz | JLIM release v2 }}
  
 Example Example
  
-{{ :jlim_2_example.tar.gz | JLIM2 example data }}+  * {{ :jlim_2_example.tar.gz | JLIM2 example data }}
  
 +Obstructive Sleep Apnea Data for Chun and Akle et al.
 +
 +  * AvSaO2: {{ :AvSaO2.sumstats.txt.gz | discovery cohort association summary statistics }} {{ :avsao2.candidate_intervals.txt.gz | candidate genomic intervals }}
 +  * MinSaO2: {{ :MinSaO2.sumstats.txt.gz | discovery cohort association summary statistics }} {{ :minsao2.candidate_intervals.txt.gz | candidate genomic intervals }}
 +  * AHI (rdi3p): {{ :rdi3p.sumstats.txt.gz | discovery cohort association summary statistics }} {{ :rdi3p.candidate_intervals.txt.gz | candidate genomic intervals }}
 +  * Event Duration: {{ :EvDur.sumstats.txt.gz | discovery cohort association summary statistics }} {{ :evdur.candidate_intervals.txt.gz | candidate genomic intervals }}
 ===== How to install ===== ===== How to install =====
  
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 ==== Excluding samples ==== ==== Excluding samples ====
 If you need to exclude any samples, you should exclude them from the secondary phenotype file, or set their phenotype to “nan”. This file can only take quantitative values (or nan). The sample file should match the genotypes in the bimbam file exactly, so no samples can be excluded from this file. If you need to exclude any samples, you should exclude them from the secondary phenotype file, or set their phenotype to “nan”. This file can only take quantitative values (or nan). The sample file should match the genotypes in the bimbam file exactly, so no samples can be excluded from this file.
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