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keller_and_evans_lab:gscan [2016/12/19 15:46] scott /* TOPMed */ |
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 ====== | ||
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+ | * **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 ====== | ||
- | 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 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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+ | * | ||
/ | / | ||
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+ | * We're tracking analyses in [[https:// | ||
===== Phenotype definitions and analysis plan for external studies ===== | ===== 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:// |