diff options
| -rw-r--r-- | doc/Architecture.org | 33 | ||||
| -rw-r--r-- | doc/database.org | 1 |
2 files changed, 27 insertions, 7 deletions
diff --git a/doc/Architecture.org b/doc/Architecture.org index cac40939..fe3eae39 100644 --- a/doc/Architecture.org +++ b/doc/Architecture.org @@ -4,7 +4,7 @@ - [[#introduction][Introduction]] - [[#webserver][Webserver]] - [[#gnserver-rest][GnServer (REST)]] - - [[#database-][Database ]] + - [[#database][Database]] - [[#phenotypes][Phenotypes]] - [[#genotypes][Genotypes]] @@ -55,7 +55,7 @@ from the database. To get the menu data in YAML you can do something like (json2yaml.rb is in the gn_server repo). For the current API definition see [[https://github.com/genenetwork/gn_server/doc/API.md][GnServer REST API]] documentation. -* Database +* Database ** Phenotypes Phenotypes are stored in the SQL database. For what happens at the @@ -66,8 +66,8 @@ see the installation [[./README.org][instructions]]. Genotypes are stored in genotype files. These are part of the GNU Guix distribution, see the installation [[./README.org][instructions]]. Genotype files are -currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2 formats]]. Now it is -for BXD.geno: +currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2 +formats]]. Currently it is for the stored file BXD.geno: #+begin_src js @name:BXD @@ -90,7 +90,28 @@ D D D D D H B D D B D B B D D B D D B B B B B B B D 1 rs6365999 0.0 4.811062 B B D D D B B D B B D D B D D D D B B B D B D D B B B B B B B B B D B D B B D B B H H B D B B H H B B D D D D D B B H B B B B D B D B D D D D D H B D D B D B B D D B D D B B B B B B U D -etc +... #+end_src -and, for example, in the method run_rqtl_geno this file gets loaded. +and, for example, in the method run_rqtl_geno this file gets +loaded. For GnServer, however, we only want to deal with standardized +R/qtl formatted data, so with gn_extra we convert the original format +into R/qtl format with geno2rqtl with one adaptation: the geno table +is transposed so now becomes + +#+begin_src js +id,BXD1,BXD2,BXD5,BXD6,BXD8,BXD9,BXD11,BXD12,BXD13,BXD14,BXD15,BXD16,BXD18,BXD19,BXD20,BXD21,BXD22,BXD23,BXD24a,BXD24,BXD25,BXD27,BXD28,BXD29,BXD30,BXD31,BXD32,BXD33,BXD34,BXD35,BXD36,BXD37,BXD38,BXD39,BXD40,BXD41,BXD42,BXD43,BXD44,BXD45,BXD48,BXD49,BXD50,BXD51,BXD52,BXD53,BXD54,BXD55,BXD56,BXD59,BXD60,BXD61,BXD62,BXD63,BXD64,BXD65,BXD66,BXD67,BXD68,BXD69,BXD70,BXD71,BXD72,BXD73,BXD74,BXD75,BXD76,BXD77,BXD78,BXD79,BXD80,BXD81,BXD83,BXD84,BXD85,BXD86,BXD87,BXD88,BXD89,BXD90,BXD91,BXD92,BXD93,BXD94,BXD95,BXD96,BXD97,BXD98,BXD99,BXD100,BXD101,BXD102,BXD103 +1,B,B,D,D,D,B,B,D,B,B,D,D,B,D,D,D,D,B,B,B,D,B,D,D,B,B,B,B,B,B,B,B,B,D,B,D,B,B,D,B,B,H,H,B,D,B,B,H,H,B,B,D,D,D,D,D,B,B,H,B,B,B,B,D,B,D,B,D,D,D,D,D,H,B,D,D,B,D,B,B,D,D,B,D,D,B,B,B,B,B,B,B,D +2,B,B,D,D,D,B,B,D,B,B,D,D,B,D,D,D,D,B,B,B,D,B,D,D,B,B,B,B,B,B,B,B,B,D,B,D,B,B,D,B,B,H,H,B,D,B,B,H,H,B,B,D,D,D,D,D,B,B,H,B,B,B,B,D,B,D,B,D,D,D,D,D,H,B,D,D,B,D,B,B,D,D,B,D,D,B,B,B,B,B,B,U,D +3,B,B,D,D,D,B,B,D,B,B,D,D,B,D,D,D,D,B,B,B,D,B,D,D,B,B,B,B,B,B,B,B,B,D,B,D,B,D,D,B,B,H,H,B,B,B,B,H,H,B,B,D,D,D,D,B,B,B,H,B,B,B,B,D,B,D,B,D,D,D,D,D,H,B,D,D,B,D,B,B,D,D,B,D,D,B,B,B,B,B,B,U,D +... +#+end_src js + +i.e. individuals are columns and markers are rows. Alternatively it could look like + +#+begin_src js +id,BXD1,BXD2,BXD5,BXD6,BXD8,BXD9,BXD11,BXD12,BXD13,BXD14,BXD15,BXD16,BXD18,BXD19,BXD20,BXD21,BXD22,BXD23,BXD24a,BXD24,BXD25,BXD27,BXD28,BXD29,BXD30,BXD31,BXD32,BXD33,BXD34,BXD35,BXD36,BXD37,BXD38,BXD39,BXD40,BXD41,BXD42,BXD43,BXD44,BXD45,BXD48,BXD49,BXD50,BXD51,BXD52,BXD53,BXD54,BXD55,BXD56,BXD59,BXD60,BXD61,BXD62,BXD63,BXD64,BXD65,BXD66,BXD67,BXD68,BXD69,BXD70,BXD71,BXD72,BXD73,BXD74,BXD75,BXD76,BXD77,BXD78,BXD79,BXD80,BXD81,BXD83,BXD84,BXD85,BXD86,BXD87,BXD88,BXD89,BXD90,BXD91,BXD92,BXD93,BXD94,BXD95,BXD96,BXD97,BXD98,BXD99,BXD100,BXD101,BXD102,BXD103 +rs6269442,B,B,D,D,D,B,B,D,B,B,D,D,B,D,D,D,D,B,B,B,D,B,D,D,B,B,B,B,B,B,B,B,B,D,B,D,B,B,D,B,B,H,H,B,D,B,B,H,H,B,B,D,D,D,D,D,B,B,H,B,B,B,B,D,B,D,B,D,D,D,D,D,H,B,D,D,B,D,B,B,D,D,B,D,D,B,B,B,B,B,B,B,D +rs6365999,B,B,D,D,D,B,B,D,B,B,D,D,B,D,D,D,D,B,B,B,D,B,D,D,B,B,B,B,B,B,B,B,B,D,B,D,B,B,D,B,B,H,H,B,D,B,B,H,H,B,B,D,D,D,D,D,B,B,H,B,B,B,B,D,B,D,B,D,D,D,D,D,H,B,D,D,B,D,B,B,D,D,B,D,D,B,B,B,B,B,B,U,D +rs6376963,B,B,D,D,D,B,B,D,B,B,D,D,B,D,D,D,D,B,B,B,D,B,D,D,B,B,B,B,B,B,B,B,B,D,B,D,B,D,D,B,B,H,H,B,B,B,B,H,H,B,B,D,D,D,D,B,B,B,H,B,B,B,B,D,B,D,B,D,D,D,D,D,H,B,D,D,B,D,B,B,D,D,B,D,D,B,B,B,B,B,B,U,D +#+end_src js diff --git a/doc/database.org b/doc/database.org index 2c7dc887..9c8c89f2 100644 --- a/doc/database.org +++ b/doc/database.org @@ -946,7 +946,6 @@ INFO:base.data_set:.sql: get_trait_info: (that is a bug!). ** Fetch phenotypes - *** Through the trait page When hitting the trait page, e.g. |