diff options
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 19 |
1 files changed, 12 insertions, 7 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index db92e14c..c2caa03e 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -275,10 +275,15 @@ 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 - r_sum = ro.r["sum"] # Map the ncol function + r_sum = ro.r["sum"] # Map the sum function print(r_library("qtl")) # Load R/qtl @@ -307,7 +312,7 @@ class MarkerRegression(object): # for debug: write_cross(cross_object, "csvr", "test.csvr") # Scan for QTLs - covar = self.create_covariates(cross_object) + covar = self.create_covariates(cross_object) # Create the additive covariate matrix if self.pair_scan: if(r_sum(covar)[0] > 0): @@ -315,20 +320,20 @@ class MarkerRegression(object): else: print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno") - print("pair scan results:", result_data_frame) + print("Pair scan results:", result_data_frame) return 0 else: if(r_sum(covar)[0] > 0): - print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar) + print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method) else: - print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno") + print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method= 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)) + perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm), model=model, method= method) else: - perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm)) + perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm), model=model, method= method) self.process_rqtl_perm_results(perm_data_frame) # Functions that sets the thresholds for the webinterface |