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keller_and_evans_lab:gscan [2016/10/24 16:25] scott |
keller_and_evans_lab:gscan [2019/10/28 15:59] (current) lessem ↷ Links adapted because of a move operation |
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====== Phenotype definitions and analysis plan ====== | ====== Phenotype definitions and analysis plan ====== | ||
- | {{file_gscan_exome_chip_analysis_plan-v2_2.pdfExome chip analysis plan and phenotype definitions.}} | + | {{:file_gscan_exome_chip_analysis_plan-v2_2.pdfexome_chip_analysis_plan_and_phenotype_definitions}} |
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======= GSCAN GWAS ======= | ======= GSCAN GWAS ======= | ||
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+ | ====== Workgroups ====== | ||
+ | |||
+ | * **Phenotype workgroup: | ||
+ | * **Analysis workgroup: | ||
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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 " | 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 " | ||
- | {{file_gscan_gwas_analysis_plan-v1_3.docxClick here to find the GSCAN GWAS analysis plan.}} | + | {{:file_gscan_gwas_analysis_plan-v1_3.docxclick_here_to_find_the_gscan_gwas_analysis_plan}} |
- | {{file_gscan_gwas_phenotype_definitions-2-24-2016.pdfClick here to find the GSCAN GWAS phenotype definitions.}} | + | {{:file_gscan_gwas_phenotype_definitions-2-24-2016.pdfclick_here_to_find_the_gscan_gwas_phenotype_definitions}} |
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====== [[gscan_db_ga_p]] & UK Biobank ====== | ====== [[gscan_db_ga_p]] & UK Biobank ====== | ||
- | Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[gscan_db_ga_p]] page. | + | Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[:gscan_db_ga_p]] page. |
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====== TOPMed ====== | ====== 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. | ||
+ | |||
+ | * For now, the R scripts to go from source phenotype file to eventual derived phenotype is located here: | ||
+ | / | ||
+ | |||
+ | * We're tracking analyses in [[https:// | ||
- | ===== Phenotype definitions and analysis plan ===== | + | ===== Phenotype definitions and analysis plan for external studies |
- | Phenotype definitions and analysis plans for the TOPMed studies are {{file_topmed_smoking_analysis_plan-v0_2.docxcontained in this document}}. | + | Phenotype definitions and analysis plans for the TOPMed studies are {{:file_topmed_smoking_analysis_plan-v0_2.docxcontained_in_this_document}}. |
The list of dbGaP studies in TOPMed is in [[https:// | The list of dbGaP studies in TOPMed is in [[https:// | ||
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- | While authorship is decided on an individual basis for each paper (depending on contribution), typically, authorship is arranged in groups. We hope the GIANT investigators will forgive us for adopting their authorship guidelines. | + | 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. |
* A group of 6 or fewer junior investigators who strongly led the efforts, usually starred to denote equal contribution, | * A group of 6 or fewer junior investigators who strongly led the efforts, usually starred to denote equal contribution, |