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keller_and_evans_lab:gscan [2016/05/02 07:42] scott /* Phenotype definitions and analysis plan */ |
keller_and_evans_lab:gscan [2019/10/28 15:59] lessem ↷ Links adapted because of a move operation |
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Regular conference calls are held and minutes are [[https:// | Regular conference calls are held and minutes are [[https:// | ||
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+ | Other meeting materials from CO internal meetings are here: | ||
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+ | [[gscan_6: | ||
======= GSCAN Exome Chip ======= | ======= GSCAN Exome Chip ======= | ||
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+ | ====== Phenotype definitions and analysis plan ====== | ||
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+ | {{: | ||
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======= GSCAN GWAS ======= | ======= GSCAN GWAS ======= | ||
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+ | ====== Workgroups ====== | ||
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+ | * **Phenotype workgroup: | ||
+ | * **Analysis workgroup: | ||
====== Phenotype definitions and analysis plan ====== | ====== Phenotype definitions and analysis plan ====== | ||
- | Click here for the GWAS analysis plan {{file_gscan_gwas_analysis_plan-v1_2.pdf}} | + | The analysis plan and phenotypes are described in files linked below (makes it easier to keep track of versioning!). Coding of phenotypes is described in the aptly-named " |
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+ | {{:file_gscan_gwas_analysis_plan-v1_3.docxclick_here_to_find_the_gscan_gwas_analysis_plan}} | ||
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+ | {{: | ||
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On RC the organization is similar. Everything is located within the folder / | On RC the organization is similar. Everything is located within the folder / | ||
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+ | ====== [[gscan_db_ga_p]] & UK Biobank ====== | ||
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+ | Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[: | ||
======= GSCAN Sequencing ======= | ======= GSCAN Sequencing ======= | ||
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+ | ====== TOPMed ====== | ||
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+ | We hope to update this section with detailed descriptions of how we have conducted phenotype derivations for each TOPMed cohort to which we have access to raw data. | ||
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+ | * For now, the R scripts to go from source phenotype file to eventual derived phenotype is located here: | ||
+ | / | ||
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+ | * We're tracking analyses in [[https:// | ||
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+ | ===== Phenotype definitions and analysis plan for external studies ===== | ||
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+ | Phenotype definitions and analysis plans for the TOPMed studies are {{: | ||
The list of dbGaP studies in TOPMed is in [[https:// | The list of dbGaP studies in TOPMed is in [[https:// | ||
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+ | ======= Authorship guidelines ======= | ||
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+ | While authorship is decided on an individual basis for each GSCAN paper, typically, authorship is arranged in groups. We hope the GIANT investigators will forgive us for adopting their authorship guidelines. | ||
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+ | * A group of 6 or fewer junior investigators who strongly led the efforts, usually starred to denote equal contribution, | ||
+ | * In alphabetical order, junior investigators who had substantial individual contributions but not as much as those in Group 1. Typically, these might be lead analysts or other junior investigators who made a sizable contribution such as GWA analyses performed specifically for the paper. | ||
+ | * In alphabetical order, junior investigators who had notable individual contributions but not as much as those in Groups 1 or 2. Typically, these might be lead analysts for replication cohorts, providing results for a group of top hits. | ||
+ | * In alphabetical order, junior and senior investigators who had contributions worthy of authorship (participating in analysis, phenotype collection, genotyping, oversight of cohorts, etc. that was specific to the paper) but not as much as those in the other groups. | ||
+ | * In alphabetical order, senior investigators who had contributions worthy of authorship and contributed more than those in group 4. Typically, these might be a lead PI of a participating cohort who did not participate as strongly in GSCAN activities as those in group 6. | ||
+ | * In alphabetical order, senior investigators who participated strongly in GSCAN activities but did not strongly lead/ | ||
+ | * The senior investigators who strongly led/oversaw the writing and/or analysis of the paper, including a subset that are co-corresponding authors (usually 6 or fewer). | ||
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