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authorPjotr Prins2016-07-26 10:49:46 +0600
committerPjotr Prins2016-07-26 10:49:46 +0600
commit41a8f2381b0d2d2f7d6aa5d50dee93d96af3ff39 (patch)
treec519471ffbaea9e28c934c8de3a156f449a63660 /doc/Architecture.org
parent48af807b4d8eabb0fac53451333fe7e85d38855b (diff)
downloadgenenetwork2-41a8f2381b0d2d2f7d6aa5d50dee93d96af3ff39.tar.gz
Docs: genotype
Diffstat (limited to 'doc/Architecture.org')
-rw-r--r--doc/Architecture.org19
1 files changed, 10 insertions, 9 deletions
diff --git a/doc/Architecture.org b/doc/Architecture.org
index e3bc8026..a1fcbef2 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -66,8 +66,9 @@ 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]]. Currently it is for the stored file BXD.geno:
+currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2 formats]].
+
+GN1-style (still default GN2) for the stored file BXD.geno:
#+begin_src js
@name:BXD
@@ -130,21 +131,21 @@ genotype data is tagged as transposed:
"founder_geno": "recla_foundergeno.csv",
"founder_geno_transposed": true,
"genotypes": {
-"1": "1",
-"2": "2",
-"3": "3"
+ "1": "1",
+ "2": "2",
+ "3": "3"
},
"pheno": "recla_pheno.csv",
"pheno_transposed": false,
"covar": "recla_covar.csv",
"sex": {
-"covar": "Sex",
-"female": "female",
-"male": "male"
+ "covar": "Sex",
+ "female": "female",
+ "male": "male"
},
"x_chr": "X",
"cross_info": {
-"covar": "ngen"
+ "covar": "ngen"
},
"gmap": "recla_gmap.csv",
"pmap": "recla_pmap.csv",