rbbt-dm 1.1.17 → 1.1.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 02a66fdb598d5f2ebbf7bdbb966e333828c25c74
-  data.tar.gz: a661e1801711f0de053b622449d0ac201cafef7e
+  metadata.gz: ba8688bb3e7913ef167e240940388ab69fa33e5c
+  data.tar.gz: 40f43f13ce557e8ae994e651cd11ab7e054ae3b0
 SHA512:
-  metadata.gz: 2dc3a421c78c79619ee01fdaadef01136da9bd6231fa8223be5184e6041e233ed2e8c7643000d055a8c79fe50c93d871fefabaaee625ac8e0bb46d57f2b20b23
-  data.tar.gz: d48a85fdbd66651cdead6cb3516c20b44f6a3190d95cfb98dad6d00434b114d96457bf7cee58b260fe5facb75ca979d5171569608108c255fdf1ea4dfe2d7a9a
+  metadata.gz: 8ed0a89e1c2d6a449b86c68536c1a55626f7a7f074714f227d8a862d1974096a40027041c254482fce4edecdd53f2518da72ce29e0ac4f106934f629fb8e29fe
+  data.tar.gz: e26cd0ce1e3ab61b2774f89f7a0c83ae63d440b4016abcb6118421a56126a21ef5f40fd1fcf3846aaa128fe508d4cffb8c89edd426affac0d36ab1002642f174

data/lib/rbbt/matrix/differential.rb

@@ -31,12 +31,18 @@ class Matrix
         log2 = true
         trend = true
         two_channel = false
-      else
+      when 'log2 ratio', 'transformed count'
         log2 = false
-        trend = true
+        trend = false
+        two_channel = false
+      else
+        Log.warn "Unkown value_type: #{value_type}"
+        log2 = true
+        trend = false
         two_channel = false
       end
 
+      file = file.find if Path === file
       FileUtils.mkdir_p File.dirname(file) unless file.nil? or File.exists? File.dirname(file)
 
       cmd = <<-EOS

data/lib/rbbt/matrix.rb

@@ -33,6 +33,10 @@ class Matrix
     @samples ||= TSV.parse_header(@data_file).fields
   end
 
+  def subsets=(subsets)
+    @subsets = subsets
+  end
+
   def subsets
     @subsets ||= begin
                    subsets = {}
@@ -138,6 +142,9 @@ class Matrix
         Misc.mean(v.compact)
       end
     end
-    Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
+    subsets = self.subsets
+    matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
+    matrix.subsets = subsets
+    matrix
   end
 end

data/lib/rbbt/statistics/random_walk.rb

@@ -276,16 +276,20 @@ module RandomWalk
     end
   end
 
-  def self.permutations_up_down(size_up, size_down, total, missing = 0, times = 10000)
-    (1..times).collect do
-      score_up_down(Array.new(size_up){ (rand * total).to_i }.sort, Array.new(size_down){ (rand * total).to_i }.sort, total, missing).abs
+  def self.persisted_permutations(size, total, missing = 0, times = 10_000)
+    require 'rbbt/util/tc_cache'
+    repo_file = "/tmp/rw_repo9"
+    key = Misc.digest([size, total, missing, times, scoring_method].inspect)
+    cache = TCCache.open(repo_file, :float_array)
+    p = cache.cache(key) do
+      permutations(size, total, missing, times)
     end
+    p
   end
 
   def self.pvalue(permutations, score)
     score = score.abs
     permutations.inject(1){|acc, per| 
-
       acc += 1 if per > score
       acc
     }.to_f / permutations.length

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.17
+  version: 1.1.18
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-11-13 00:00:00.000000000 Z
+date: 2015-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util