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--- keller_and_evans_lab:gscan [2016/11/09 07:54]
scott /* Authorship guidelines */
+++ keller_and_evans_lab:gscan [2019/10/28 15:59] (current)
lessem ↷ Links adapted because of a move operation
@@ Line 18: / Line 18: @@
 ====== 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}}
@@ Line 29: / Line 29: @@
 ======= GSCAN GWAS =======
+====== Workgroups ======
+  * **Phenotype workgroup:** Laura Bierut, Marilyn Cornelis, Dave Hinds, Youna Hu, Jaakko Kaprio, Eric Jorgenson, Dajiang Liu, Matt McGue, Marcus Munafo, Gunter Schumann, Scott Vrieze, Luisa Zuccolo
+  * **Analysis workgroup:** Goncalo Abecasis, David Hinds, Youna Hu, Eric Jorgenson, Charles Kooperberg, Pete Kraft, Penelope Lind, Dajiang Liu, Nancy Saccone, Dan Stram, Scott Vrieze, Xiaowei Zhan
@@ Line 35: / Line 41: @@
 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}}
@@ Line 58: / Line 64: @@
 ====== [[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.
@@ Line 65: / Line 71: @@
 ====== 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:
+  /net/twins/svrieze/everything-else/wp/GSCAN/TOPMed/README
+  *  We're tracking analyses in [[https://docs.google.com/document/d/1HtJY6DzPWqr2XGTAD8HzoiIUoC45nSj116neRb3do3s/edit|**this Google doc**]]
-===== 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://airtable.com/shryD6CMaM6R5sA3e/tblUKENXX5WmgNXQ8|**this Airtable**]].

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