rbbt-dm 1.1.1 → 1.1.2

checksums.yaml

@@ -1,15 +1,7 @@
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+SHA1:
+  metadata.gz: 3b56aaf594c49cc2f9797e91bf732ba5014c0040
+  data.tar.gz: f229787d7456462c0ee538c19fd7f22750acb78d
+SHA512:
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+  data.tar.gz: 01a7d232b15db85af6f8d00c4b4d329895b41ab207521a249f62059337f7fe89a3ef11fa1188f2f6346379a3ee7c111b210ff954b1bbfc9b6b43bfbdbe238d64

data/lib/rbbt/statistics/fdr.rb

@@ -34,19 +34,19 @@ module FDR
   inline do |builder|
 
     builder.prefix  <<-EOC_CODE
+
 //{{{ Make compatible with 1.9 and 1.8
 #ifndef RUBY_19
-#ifndef RFLOAT_VALUE
-#define RFLOAT_VALUE(v) (RFLOAT(v)->value)
-#endif
-#ifndef RARRAY_PTR
-#define RARRAY_PTR(v) (RARRAY(v)->ptr)
-#endif
-#ifndef RARRAY_LEN
-#define RARRAY_LEN(v) (RARRAY(v)->len)
+# define RFLOAT_VALUE_SET(v) (((struct RFloat *)v)->float_value)
+# ifndef RFLOAT_VALUE
+#  define RFLOAT_VALUE(v) (RFLOAT(v)->value)
+# endif
+# ifndef RARRAY_LEN
+#  define RARRAY_LEN(v) (RARRAY(v)->len)
+# endif
+#else
+# define RFLOAT_VALUE_SET(v) RFLOAT_VALUE
 #endif
-#endif
-//}}} Make compatible with 1.9 and 1.8
     EOC_CODE
 
     c_code = <<-EOC_CODE
@@ -55,8 +55,10 @@ module FDR
            int total = (int) RARRAY_LEN(ps);
 
            double last_value = 0;
+           double p;
+
            for (idx = 0; idx < total; idx++){
-             double p  = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
+             p  = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
 
              if (p > rate * (double) (idx + 1) / (double) total){
                 return last_value;
@@ -76,18 +78,18 @@ module FDR
 
            int total = (int) RARRAY_LEN(ps);
 
-           VALUE new = rb_ary_new();
-
            double last = 1;
+           VALUE current_value;
            for (idx = total - 1; idx >= 0 ; idx-- ){
-             double p  = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
-
+             current_value = rb_ary_entry(ps, idx);
+             
+             double p  = (double) RFLOAT_VALUE(current_value);
 
              p = p * (double) total / (double) (idx + 1);
              if (p > last) p = last;
              last = p;
 
-             RFLOAT_VALUE(rb_ary_entry(ps, idx)) = p;
+             RFLOAT_VALUE_SET(rb_ary_entry(ps, idx)) = p;
            }
 
           return ps;
@@ -101,21 +103,24 @@ module FDR
 
            int total = (int) RARRAY_LEN(ps);
 
-           VALUE new = rb_ary_new();
+           VALUE new_ary = rb_ary_new();
+           VALUE f;
+
+           double p, last = 1;
 
-           double last = 1;
            for (idx = total - 1; idx >= 0 ; idx-- ){
-             double p  = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
+             p  = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
 
 
              p = p * (double) total / (double) (idx + 1);
              if (p > last) p = last;
              last = p;
 
-             rb_ary_unshift(new,rb_float_new(p));
+             f = rb_float_new(p);
+             rb_ary_unshift(new_ary, f);
            }
 
-           return new;
+           return new_ary;
          }
     EOC_CODE
     builder.c_singleton c_code
@@ -130,7 +135,7 @@ module FDR
     alias :step_up :step_up_fast
   end
 
-  # This will change the values of the floats in situ
+  # This will change the values of the floats in-situ
   def self.adjust_hash!(data, field = nil)
     keys = []
     values = []
@@ -151,9 +156,15 @@ module FDR
       data.unnamed = unnamed
     end
 
-    FDR.adjust!(values)
+    if RUBY_VERSION[0] == "2"
+      # I don't know why the RFLOAT_VALUE_SET for Ruby 2.1.0 does not work
+      values = FDR.adjust(values)
+      data   = Hash[*keys.zip(values).flatten]
+    else
+      FDR.adjust!(values)
+    end
 
-    data
+    data 
   end
 
 end

data/lib/rbbt/statistics/hypergeometric.rb

@@ -249,7 +249,7 @@ module TSV
         pvalues[annotation] = RSRuby.instance.phyper(count - 1, counts[annotation], tsv_size - counts[annotation], total, false).to_f
       end
 
-      FDR.adjust_hash! pvalues if options[:fdr]
+      pvalues = FDR.adjust_hash! pvalues if options[:fdr]
 
       pvalues.delete_if{|k, pvalue| pvalue > options[:cutoff] } if options[:cutoff]
 

metadata

@@ -1,83 +1,83 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.1
+  version: 1.1.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-03 00:00:00.000000000 Z
+date: 2014-01-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: RubyInline
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: priority_queue
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: distribution
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: png
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 description: Data-mining and statistics
@@ -100,12 +100,12 @@ files:
 - lib/rbbt/statistics/rank_product.rb
 - lib/rbbt/vector/model.rb
 - lib/rbbt/vector/model/svm.rb
+- test/rbbt/network/test_paths.rb
+- test/rbbt/statistics/test_fdr.rb
 - test/rbbt/statistics/test_hypergeometric.rb
 - test/rbbt/statistics/test_random_walk.rb
-- test/rbbt/statistics/test_fdr.rb
-- test/rbbt/network/test_paths.rb
-- test/rbbt/vector/test_model.rb
 - test/rbbt/vector/model/test_svm.rb
+- test/rbbt/vector/test_model.rb
 - test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-phgx
 licenses: []
@@ -116,25 +116,25 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
 summary: Data-mining and statistics
 test_files:
-- test/rbbt/statistics/test_hypergeometric.rb
-- test/rbbt/statistics/test_random_walk.rb
-- test/rbbt/statistics/test_fdr.rb
 - test/rbbt/network/test_paths.rb
-- test/rbbt/vector/test_model.rb
+- test/rbbt/statistics/test_fdr.rb
+- test/rbbt/statistics/test_random_walk.rb
+- test/rbbt/statistics/test_hypergeometric.rb
 - test/rbbt/vector/model/test_svm.rb
+- test/rbbt/vector/test_model.rb
 - test/test_helper.rb