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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py17
1 files changed, 8 insertions, 9 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index c2caa03e..d2df5cd1 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -83,6 +83,10 @@ class MarkerRegression(object):
self.num_perm = start_vars['num_perm']
self.control = start_vars['control_marker']
+ self.method = start_vars['method_rqtl']
+ self.model = start_vars['model_rqtl']
+
+
if start_vars['pair_scan'] == "true":
self.pair_scan = True
else:
@@ -275,11 +279,6 @@ class MarkerRegression(object):
self.geno_to_rqtl_function()
- #Danny @t Zachary, these two additional parameters should be be provided by the user, they can be drop down options in the interface
-
- model = "normal" # Model can be "normal","binary","2part","np"
- method = "em" # Method can be "em","imp","hk","ehk","mr","mr-imp","mr-argmax"
-
## Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
@@ -325,15 +324,15 @@ class MarkerRegression(object):
return 0
else:
if(r_sum(covar)[0] > 0):
- print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
+ print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method)
else:
- print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method= method)
+ print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=self.model, method=self.method)
if int(self.num_perm) > 0: # Do permutation (if requested by user)
if(r_sum(covar)[0] > 0):
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm), model=model, method= method)
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm), model=self.model, method=self.method)
else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm), model=model, method= method)
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm), model=self.model, method=self.method)
self.process_rqtl_perm_results(perm_data_frame) # Functions that sets the thresholds for the webinterface