rbbt-dm 1.1.4 → 1.1.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: b8015384a48dd97d9aaacc87f409d4a003b6a25e
+  metadata.gz: 8e5a9283f6f9108886ee24aeea8b589e6499833f
+  data.tar.gz: 171269f201ce1e0f6d068e0002096cd94884150a
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+  data.tar.gz: c7e7e6bf19b44a2ba0638df98d515e7239da9e1933f77cf7ed93552caae60dde9b66b53056d2eacd692ec51b2023c0894cfb435a7eaec92954fda4963dadc71c

data/lib/rbbt/statistics/fdr.rb

@@ -135,36 +135,48 @@ module FDR
     alias :step_up :step_up_fast
   end
 
-  # This will change the values of the floats in-situ
   def self.adjust_hash!(data, field = nil)
-    keys = []
-    values = []
-
-    if data.respond_to? :unnamed
-      unnamed = data.unnamed 
-      data.unnamed = true
-    end
-
-    data.collect{|key, value| [key, Array === ( v = field.nil? ? value : value[field] ) ? v.first : v] }.sort{|a,b| 
-      a[1] <=> b[1]
-    }.each{|p|
-      keys << p[0]
-      values << p[1]
-    }
+    begin
+      if data.respond_to? :unnamed
+        unnamed = data.unnamed 
+        data.unnamed = true
+      end
 
-    if data.respond_to? :unnamed
-      data.unnamed = unnamed
-    end
+      values = []
+      keys = []
+      data.collect{|k,vs|
+        v = field.nil? ? vs : vs[field]
+        v = v.first if Array === v
+        [k, v] 
+      }.sort{|a,b| 
+        a[1] <=> b[1]
+      }.each{|p|
+        keys << p[0]
+        values << p[1]
+      }
+
+      if RUBY_VERSION[0] == "2"
+        values = FDR.adjust(values)
+        keys.zip(values).each do |k,v|
+          vs = data[k] 
+          if field
+            vs[field] = v
+          else
+            if Array === vs
+              vs[0] = v
+            else
+              data[k] = vs
+            end
+          end
+        end
+      else
+        FDR.adjust!(values)
+      end
 
-    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)
+      data
+    ensure
+      data.unnamed = unnamed if unnamed
     end
-
-    data 
   end
 
 end

data/lib/rbbt/statistics/hypergeometric.rb

@@ -101,8 +101,9 @@ double hypergeometric_c(double total, double support, double list, double found)
     EOC
   end
 
-  def self.hypergeometric(total, support, list, found)
-    RSRuby.instance.phyper(found, support, total - support, list, false).to_f
+  def self.hypergeometric(count, positive, negative, total)
+    #RSRuby.instance.phyper(count - 1, positive, negative, total, false).to_f
+    R.eval("phyper(#{ count } - 1, #{ positive }, #{ negative }, #{ total }, FALSE)").to_f
   end
 end
 
@@ -246,7 +247,8 @@ module TSV
         elems = elems.collect{|elem| rename.include?(elem)? rename[elem] : elem }.compact.uniq if rename
         count = elems.length
         next if count < options[:min_support] or not counts.include? annotation
-        pvalues[annotation] = RSRuby.instance.phyper(count - 1, counts[annotation], tsv_size - counts[annotation], total, false).to_f
+        #pvalues[annotation] = RSRuby.instance.phyper(count - 1, counts[annotation], tsv_size - counts[annotation], total, false).to_f
+        pvalues[annotation] = Hypergeometric.hypergeometric(count, counts[annotation], tsv_size - counts[annotation], total)
       end
 
       pvalues = FDR.adjust_hash! pvalues if options[:fdr]

data/test/rbbt/statistics/test_fdr.rb

@@ -1,7 +1,7 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/statistics/fdr'
 require 'test/unit'
-require 'rsruby'
+require 'rbbt/util/R'
 
 class TestFDR < Test::Unit::TestCase
   def clean(values)
@@ -17,11 +17,9 @@ class TestFDR < Test::Unit::TestCase
   end
 
   def setup
-    @r = RSRuby.instance
     @values = [0.001, 0.002, 0.003, 0.003, 0.003, 0.004, 0.006, 0.07, 0.09]
     @threshold = 0.01
-    @r_adj = @r.p_adjust(@values,'BH')
-
+    @r_adj = R.eval_a "p.adjust(#{R.ruby2R(@values)},'BH')"
   end
 
   def test_step_up
@@ -34,8 +32,9 @@ class TestFDR < Test::Unit::TestCase
     assert_equal(clean(@r_adj), clean(FDR.adjust_native(@values)))
     assert_equal(clean(FDR.adjust_fast(@values)), clean(FDR.adjust_native(@values)))
 
-    assert_equal(clean(@r_adj), clean(FDR.adjust_fast_self(copy(@values))))
+    assert_equal(clean(@r_adj), clean(FDR.adjust_fast_self(copy(@values)))) if RUBY_VERSION[0] != "2"
   end
+
 end
 
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.4
+  version: 1.1.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-25 00:00:00.000000000 Z
+date: 2014-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util