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-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py29
1 files changed, 0 insertions, 29 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 5511826a..4b4b7f73 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -24,9 +24,6 @@ from base import data_set
from base import species
from base import webqtlConfig
from utility import webqtlUtil
-from wqflask.my_pylmm.data import prep_data
-from wqflask.my_pylmm.pyLMM import lmm
-from wqflask.my_pylmm.pyLMM import input
from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
@@ -223,32 +220,6 @@ class IntervalMapping(object):
"cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive}
self.qtl_results.append(qtl)
- def gen_pylmm_results(self, tempdata):
- print("USING PYLMM")
- self.dataset.group.get_markers()
-
- pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
- if self.dataset.group.species == "human":
- p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
- else:
- genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-
- no_val_samples = self.identify_empty_samples()
- trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-
- genotype_matrix = np.array(trimmed_genotype_data).T
-
- t_stats, p_values = lmm.run(
- pheno_vector,
- genotype_matrix,
- restricted_max_likelihood=True,
- refit=False,
- temp_data=tempdata
- )
-
- print("p_values:", p_values)
- self.dataset.group.markers.add_pvalues(p_values)
- self.qtl_results = self.dataset.group.markers.markers
def gen_qtl_results_2(self, tempdata):
"""Generates qtl results for plotting interval map"""