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-rw-r--r--doc/Architecture.org19
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py2
2 files changed, 11 insertions, 10 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",
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9573a9de..33ebc527 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -382,7 +382,7 @@ class MarkerRegression(object):
self.GraphInterval = self.MbGraphInterval #Mb
else:
self.GraphInterval = self.cMGraphInterval #cM
-
+
################################################################
# Get Trait Values and Infomation
################################################################