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authorDanny Arends2020-05-06 12:06:40 -0500
committerDanny Arends2020-05-06 12:06:40 -0500
commitbcd0110bbf8d3e290023891852c21de3d5b7ebc6 (patch)
treeaec55996a344f7449465c54f0af20113bfb2768c /wqflask
parent5620f395c6a38f961ee221ed6abf4aee1fb21bfa (diff)
downloadgenenetwork2-bcd0110bbf8d3e290023891852c21de3d5b7ebc6.tar.gz
Put in TODOs for MariaDB query and Design Matrix
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py7
1 files changed, 4 insertions, 3 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 152bb5be..4070e9f5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -62,6 +62,7 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
logger.info("Marker covars done");
if cofactors != "":
+ logger.info("Cofactors: " + cofactors);
cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
@@ -71,7 +72,6 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
#logger.info("Saving Done");
covars = ro.r['all_covars']
#DEBUG to save the session object to file
- #ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")')
if pair_scan:
if do_control == "true":
logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
@@ -274,7 +274,8 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_name_string += ")"
covars_ob = pull_var("trait_covars", cross, covar_name_string)
-
+ # TODO: Pull in the types of the covars from MariaDB
+ # TODO: Iterate through the covar types and create a design matrix based on it
return cross, covars_ob
def create_marker_covariates(control_marker, cross):
@@ -287,7 +288,7 @@ def create_marker_covariates(control_marker, cross):
ro.r('covnames <- covnames[covInGeno]')
ro.r("cat('covnames (purged): ', covnames,'\n')")
ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
-
+ # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
return ro.r["marker_covars"]
def process_pair_scan_results(result):