diff options
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 17 |
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 |