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| author | Pjotr Prins | 2016-07-26 10:49:46 +0600 |
|---|---|---|
| committer | Pjotr Prins | 2016-07-26 10:49:46 +0600 |
| commit | 41a8f2381b0d2d2f7d6aa5d50dee93d96af3ff39 (patch) | |
| tree | c519471ffbaea9e28c934c8de3a156f449a63660 | |
| parent | 48af807b4d8eabb0fac53451333fe7e85d38855b (diff) | |
| download | genenetwork2-41a8f2381b0d2d2f7d6aa5d50dee93d96af3ff39.tar.gz | |
Docs: genotype
| -rw-r--r-- | doc/Architecture.org | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 2 |
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 ################################################################ |