fix for set enrichment

- bonferroni cutoff: fixed order of denominator/numerator - updated changes - updated version number and README
baliga-lab · Aug 22, 2016 · f663616 · f663616
1 parent b23c1f0
commit f663616
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,14 @@
 Changes
 =======
 
+Version 1.2.0, 2016/08/22
+-------------------------
+
+  - fix: numeric row names are converted to string
+  - fix: DataMatrix.subtract_with_quantile() did not have any effect
+  - fix: set enrichment, bonferroni cutoff denominator-numerator were
+    in wrong positions
+
 Version 1.2.0, 2016/08/08
 -------------------------
 

diff --git a/README.md b/README.md
@@ -126,6 +126,14 @@ Running cMonkey on Human data is somewhat difficult because neither the string d
 
 ### Package maintainers
 
+#### General
+
+The distribution is built using setuptools and wheel format
+
+  - setup.py contains all information needed to build the distribution
+    increase the version number before making a distribution
+  - record user-relevant changes in CHANGELOG.rst
+
 #### Build distribution
 
 python3 setup.py sdist bdist_wheel

diff --git a/cmonkey/set_enrichment.py b/cmonkey/set_enrichment.py
@@ -188,7 +188,7 @@ def __init__(self, organism, membership, ratios, config_params=None):
 
     def bonferroni_cutoff(self):
         """Bonferroni cutoff value"""
-        return float(self.num_clusters()) / 0.05
+        return 0.05 / float(self.num_clusters())
 
     def do_compute(self, iteration_result, ref_matrix):
         """compute method
@@ -229,15 +229,16 @@ def do_compute(self, iteration_result, ref_matrix):
             SET_SET_TYPE = set_type
             logging.info("PROCESSING SET TYPE '%s'", set_type.name)
             start1 = util.current_millis()
+            cutoff = self.bonferroni_cutoff()
             if use_multiprocessing:
                 with util.get_mp_pool(self.config_params) as pool:
                     results = pool.map(compute_cluster_score,
-                                       [(cluster, self.bonferroni_cutoff(), ref_min_score)
+                                       [(cluster, cutoff, ref_min_score)
                                         for cluster in xrange(1, self.num_clusters() + 1)])
             else:
                 results = []
                 for cluster in xrange(1, self.num_clusters() + 1):
-                    results.append(compute_cluster_score((cluster, self.bonferroni_cutoff(), ref_min_score)))
+                    results.append(compute_cluster_score((cluster, cutoff, ref_min_score)))
 
             elapsed1 = util.current_millis() - start1
             logging.info("ENRICHMENT SCORES COMPUTED in %f s, STORING...",

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
 LICENSE = 'LGPL V3'
 URI = 'https://github.com/baliga-lab/cmonkey2'
 AUTHOR = 'Baliga Lab, Institute for Systems Biology'
-VERSION = '1.2.0'
+VERSION = '1.2.1'
 
 KEYWORDS = ['class', 'cmonkey2']