rbbt-dm 1.1.1 → 1.1.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. checksums.yaml +6 -14
  2. data/lib/rbbt/statistics/fdr.rb +35 -24
  3. data/lib/rbbt/statistics/hypergeometric.rb +1 -1
  4. metadata +22 -22
checksums.yaml CHANGED
@@ -1,15 +1,7 @@
1
1
  ---
2
- !binary "U0hBMQ==":
3
- metadata.gz: !binary |-
4
- ZmUyMjZiODkyY2RmODNkMmNkMGJmYWZiYWFmMThkMDIzOGIzZDE5OA==
5
- data.tar.gz: !binary |-
6
- MTQ4MjdiZDY3YTljZTU2ZTViODVjNjA1NTdmYTY1MDQ2OWMxYmIzNg==
7
- !binary "U0hBNTEy":
8
- metadata.gz: !binary |-
9
- MjBjZGUxNzk2Y2M1NDU1MzNmZmI1MTk3ODdhOTMxMjA4Njk5NzhkNGM4Mjhh
10
- ODZmZmNiOWRjZGQ2ZjBlYTMzMDliZDM2ZDBkYjMzNDA2MThkNjdmNzJmOTNh
11
- MmRmN2Y5MzEzOGM0MDUwNWQzYzE2YmVjYTdjMmMzMzk0MTNhNjQ=
12
- data.tar.gz: !binary |-
13
- NTZkZGFiODMwZTljNDNhYzEyMWJiYzljNGE4OWYzNTFkNjg2OGRjY2Q1ZDQ5
14
- Y2QwZjMwNzgzNmUyYzI1NmJjNzkyYjhhZDU2M2ZmZjU0ZWY4Mjg3NGYxOGU4
15
- YTNmN2ZhYzhkMGQ1NWYxNjhjY2FkMzIzOGQwMWI5M2M0ZDE4NzU=
2
+ SHA1:
3
+ metadata.gz: 3b56aaf594c49cc2f9797e91bf732ba5014c0040
4
+ data.tar.gz: f229787d7456462c0ee538c19fd7f22750acb78d
5
+ SHA512:
6
+ metadata.gz: 1a26e288df24cbf18bc1b499ebc392e0310ed7447ad8c7ae7c14cabdfb56ecb79143c09c6441593711d30c441742b95d9eea6ab611d5745e7acf24d66dff2234
7
+ data.tar.gz: 01a7d232b15db85af6f8d00c4b4d329895b41ab207521a249f62059337f7fe89a3ef11fa1188f2f6346379a3ee7c111b210ff954b1bbfc9b6b43bfbdbe238d64
data/lib/rbbt/statistics/fdr.rb CHANGED
@@ -34,19 +34,19 @@ module FDR
34
34
  inline do |builder|
35
35
 
36
36
  builder.prefix <<-EOC_CODE
37
+
37
38
  //{{{ Make compatible with 1.9 and 1.8
38
39
  #ifndef RUBY_19
39
- #ifndef RFLOAT_VALUE
40
- #define RFLOAT_VALUE(v) (RFLOAT(v)->value)
41
- #endif
42
- #ifndef RARRAY_PTR
43
- #define RARRAY_PTR(v) (RARRAY(v)->ptr)
44
- #endif
45
- #ifndef RARRAY_LEN
46
- #define RARRAY_LEN(v) (RARRAY(v)->len)
40
+ # define RFLOAT_VALUE_SET(v) (((struct RFloat *)v)->float_value)
41
+ # ifndef RFLOAT_VALUE
42
+ # define RFLOAT_VALUE(v) (RFLOAT(v)->value)
43
+ # endif
44
+ # ifndef RARRAY_LEN
45
+ # define RARRAY_LEN(v) (RARRAY(v)->len)
46
+ # endif
47
+ #else
48
+ # define RFLOAT_VALUE_SET(v) RFLOAT_VALUE
47
49
  #endif
48
- #endif
49
- //}}} Make compatible with 1.9 and 1.8
50
50
  EOC_CODE
51
51
 
52
52
  c_code = <<-EOC_CODE
@@ -55,8 +55,10 @@ module FDR
55
55
  int total = (int) RARRAY_LEN(ps);
56
56
 
57
57
  double last_value = 0;
58
+ double p;
59
+
58
60
  for (idx = 0; idx < total; idx++){
59
- double p = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
61
+ p = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
60
62
 
61
63
  if (p > rate * (double) (idx + 1) / (double) total){
62
64
  return last_value;
@@ -76,18 +78,18 @@ module FDR
76
78
 
77
79
  int total = (int) RARRAY_LEN(ps);
78
80
 
79
- VALUE new = rb_ary_new();
80
-
81
81
  double last = 1;
82
+ VALUE current_value;
82
83
  for (idx = total - 1; idx >= 0 ; idx-- ){
83
- double p = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
84
-
84
+ current_value = rb_ary_entry(ps, idx);
85
+
86
+ double p = (double) RFLOAT_VALUE(current_value);
85
87
 
86
88
  p = p * (double) total / (double) (idx + 1);
87
89
  if (p > last) p = last;
88
90
  last = p;
89
91
 
90
- RFLOAT_VALUE(rb_ary_entry(ps, idx)) = p;
92
+ RFLOAT_VALUE_SET(rb_ary_entry(ps, idx)) = p;
91
93
  }
92
94
 
93
95
  return ps;
@@ -101,21 +103,24 @@ module FDR
101
103
 
102
104
  int total = (int) RARRAY_LEN(ps);
103
105
 
104
- VALUE new = rb_ary_new();
106
+ VALUE new_ary = rb_ary_new();
107
+ VALUE f;
108
+
109
+ double p, last = 1;
105
110
 
106
- double last = 1;
107
111
  for (idx = total - 1; idx >= 0 ; idx-- ){
108
- double p = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
112
+ p = (double) RFLOAT_VALUE(rb_ary_entry(ps, idx));
109
113
 
110
114
 
111
115
  p = p * (double) total / (double) (idx + 1);
112
116
  if (p > last) p = last;
113
117
  last = p;
114
118
 
115
- rb_ary_unshift(new,rb_float_new(p));
119
+ f = rb_float_new(p);
120
+ rb_ary_unshift(new_ary, f);
116
121
  }
117
122
 
118
- return new;
123
+ return new_ary;
119
124
  }
120
125
  EOC_CODE
121
126
  builder.c_singleton c_code
@@ -130,7 +135,7 @@ module FDR
130
135
  alias :step_up :step_up_fast
131
136
  end
132
137
 
133
- # This will change the values of the floats in situ
138
+ # This will change the values of the floats in-situ
134
139
  def self.adjust_hash!(data, field = nil)
135
140
  keys = []
136
141
  values = []
@@ -151,9 +156,15 @@ module FDR
151
156
  data.unnamed = unnamed
152
157
  end
153
158
 
154
- FDR.adjust!(values)
159
+ if RUBY_VERSION[0] == "2"
160
+ # I don't know why the RFLOAT_VALUE_SET for Ruby 2.1.0 does not work
161
+ values = FDR.adjust(values)
162
+ data = Hash[*keys.zip(values).flatten]
163
+ else
164
+ FDR.adjust!(values)
165
+ end
155
166
 
156
- data
167
+ data
157
168
  end
158
169
 
159
170
  end
data/lib/rbbt/statistics/hypergeometric.rb CHANGED
@@ -249,7 +249,7 @@ module TSV
249
249
  pvalues[annotation] = RSRuby.instance.phyper(count - 1, counts[annotation], tsv_size - counts[annotation], total, false).to_f
250
250
  end
251
251
 
252
- FDR.adjust_hash! pvalues if options[:fdr]
252
+ pvalues = FDR.adjust_hash! pvalues if options[:fdr]
253
253
 
254
254
  pvalues.delete_if{|k, pvalue| pvalue > options[:cutoff] } if options[:cutoff]
255
255
 
metadata CHANGED
@@ -1,83 +1,83 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-dm
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.1.1
4
+ version: 1.1.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2013-11-03 00:00:00.000000000 Z
11
+ date: 2014-01-20 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rbbt-util
15
15
  requirement: !ruby/object:Gem::Requirement
16
16
  requirements:
17
- - - ! '>='
17
+ - - ">="
18
18
  - !ruby/object:Gem::Version
19
19
  version: '0'
20
20
  type: :runtime
21
21
  prerelease: false
22
22
  version_requirements: !ruby/object:Gem::Requirement
23
23
  requirements:
24
- - - ! '>='
24
+ - - ">="
25
25
  - !ruby/object:Gem::Version
26
26
  version: '0'
27
27
  - !ruby/object:Gem::Dependency
28
28
  name: RubyInline
29
29
  requirement: !ruby/object:Gem::Requirement
30
30
  requirements:
31
- - - ! '>='
31
+ - - ">="
32
32
  - !ruby/object:Gem::Version
33
33
  version: '0'
34
34
  type: :runtime
35
35
  prerelease: false
36
36
  version_requirements: !ruby/object:Gem::Requirement
37
37
  requirements:
38
- - - ! '>='
38
+ - - ">="
39
39
  - !ruby/object:Gem::Version
40
40
  version: '0'
41
41
  - !ruby/object:Gem::Dependency
42
42
  name: priority_queue
43
43
  requirement: !ruby/object:Gem::Requirement
44
44
  requirements:
45
- - - ! '>='
45
+ - - ">="
46
46
  - !ruby/object:Gem::Version
47
47
  version: '0'
48
48
  type: :runtime
49
49
  prerelease: false
50
50
  version_requirements: !ruby/object:Gem::Requirement
51
51
  requirements:
52
- - - ! '>='
52
+ - - ">="
53
53
  - !ruby/object:Gem::Version
54
54
  version: '0'
55
55
  - !ruby/object:Gem::Dependency
56
56
  name: distribution
57
57
  requirement: !ruby/object:Gem::Requirement
58
58
  requirements:
59
- - - ! '>='
59
+ - - ">="
60
60
  - !ruby/object:Gem::Version
61
61
  version: '0'
62
62
  type: :runtime
63
63
  prerelease: false
64
64
  version_requirements: !ruby/object:Gem::Requirement
65
65
  requirements:
66
- - - ! '>='
66
+ - - ">="
67
67
  - !ruby/object:Gem::Version
68
68
  version: '0'
69
69
  - !ruby/object:Gem::Dependency
70
70
  name: png
71
71
  requirement: !ruby/object:Gem::Requirement
72
72
  requirements:
73
- - - ! '>='
73
+ - - ">="
74
74
  - !ruby/object:Gem::Version
75
75
  version: '0'
76
76
  type: :runtime
77
77
  prerelease: false
78
78
  version_requirements: !ruby/object:Gem::Requirement
79
79
  requirements:
80
- - - ! '>='
80
+ - - ">="
81
81
  - !ruby/object:Gem::Version
82
82
  version: '0'
83
83
  description: Data-mining and statistics
@@ -100,12 +100,12 @@ files:
100
100
  - lib/rbbt/statistics/rank_product.rb
101
101
  - lib/rbbt/vector/model.rb
102
102
  - lib/rbbt/vector/model/svm.rb
103
+ - test/rbbt/network/test_paths.rb
104
+ - test/rbbt/statistics/test_fdr.rb
103
105
  - test/rbbt/statistics/test_hypergeometric.rb
104
106
  - test/rbbt/statistics/test_random_walk.rb
105
- - test/rbbt/statistics/test_fdr.rb
106
- - test/rbbt/network/test_paths.rb
107
- - test/rbbt/vector/test_model.rb
108
107
  - test/rbbt/vector/model/test_svm.rb
108
+ - test/rbbt/vector/test_model.rb
109
109
  - test/test_helper.rb
110
110
  homepage: http://github.com/mikisvaz/rbbt-phgx
111
111
  licenses: []
@@ -116,25 +116,25 @@ require_paths:
116
116
  - lib
117
117
  required_ruby_version: !ruby/object:Gem::Requirement
118
118
  requirements:
119
- - - ! '>='
119
+ - - ">="
120
120
  - !ruby/object:Gem::Version
121
121
  version: '0'
122
122
  required_rubygems_version: !ruby/object:Gem::Requirement
123
123
  requirements:
124
- - - ! '>='
124
+ - - ">="
125
125
  - !ruby/object:Gem::Version
126
126
  version: '0'
127
127
  requirements: []
128
128
  rubyforge_project:
129
- rubygems_version: 2.0.3
129
+ rubygems_version: 2.2.1
130
130
  signing_key:
131
131
  specification_version: 4
132
132
  summary: Data-mining and statistics
133
133
  test_files:
134
- - test/rbbt/statistics/test_hypergeometric.rb
135
- - test/rbbt/statistics/test_random_walk.rb
136
- - test/rbbt/statistics/test_fdr.rb
137
134
  - test/rbbt/network/test_paths.rb
138
- - test/rbbt/vector/test_model.rb
135
+ - test/rbbt/statistics/test_fdr.rb
136
+ - test/rbbt/statistics/test_random_walk.rb
137
+ - test/rbbt/statistics/test_hypergeometric.rb
139
138
  - test/rbbt/vector/model/test_svm.rb
139
+ - test/rbbt/vector/test_model.rb
140
140
  - test/test_helper.rb