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keller_and_evans_lab:gscan [2019/10/28 21:59] – ↷ Page moved from gscan to keller_and_evans_lab:gscan lessemkeller_and_evans_lab:gscan [2019/10/28 21:59] (current) – ↷ Links adapted because of a move operation lessem
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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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 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 "phenotype definitions" file whereas the genome-wide analysis plan is in the all-too-aptly-named "analysis plan" document. Please note that the phenotype definitions document only contains information on how to code the eight smoking/drinking phenotypes. File formats for those phenotypes, which many will recognize as standard pedigree formats, are included in the analysis plan. Everything else should be fairly straightforward. 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 "phenotype definitions" file whereas the genome-wide analysis plan is in the all-too-aptly-named "analysis plan" document. Please note that the phenotype definitions document only contains information on how to code the eight smoking/drinking phenotypes. File formats for those phenotypes, which many will recognize as standard pedigree formats, are included in the analysis plan. Everything else should be fairly straightforward.
  
-{{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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 ===== 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://airtable.com/shryD6CMaM6R5sA3e/tblUKENXX5WmgNXQ8|**this Airtable**]]. The list of dbGaP studies in TOPMed is in [[https://airtable.com/shryD6CMaM6R5sA3e/tblUKENXX5WmgNXQ8|**this Airtable**]].
keller_and_evans_lab/gscan.1572299965.txt.gz · Last modified: by lessem