rbbt-dm 1.1.13 → 1.1.14
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- checksums.yaml +4 -4
- data/lib/rbbt/matrix.rb +3 -3
- data/lib/rbbt/matrix/differential.rb +4 -2
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: c2b26e9957f7e161566093695ef9e6041be4e074
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4
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+
data.tar.gz: 16e52936efa8d8a8a80a998caf6d6f9b498600aa
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 1ccf87c9524a4280fd691501ad6375d9375a2f0fb9e1ffa49221a3c891e1606670fa9f5d2a0e506144717e37bb1935febb505b858f330b1161df332ce2957b0c
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7
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+
data.tar.gz: 9ef1e9c5e5fb08e4cfdec45605d1ad6e1745b8ad4e0a9d685cbf78d2cb6c04895b54be1f4588f18b709d86b2a039176bc2a6de24a0fb1684656b19c7a2d9f350
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data/lib/rbbt/matrix.rb
CHANGED
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@@ -24,7 +24,7 @@ class Matrix
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24
24
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_header = nil
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25
25
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@organism ||= begin
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26
26
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_header ||= TSV.parse_header(@data_file)
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27
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-
_header.namespace || "Hsa"
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27
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+
_header.namespace || Organism.default_code("Hsa")
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28
28
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end
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29
29
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@identifiers = identifiers
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30
30
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end
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@@ -110,7 +110,7 @@ class Matrix
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110
110
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contrast_samples = contrast.split(/[|,\n]/)
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111
111
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end
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112
112
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else
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113
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-
if subsets and
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113
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+
if subsets and main_factor
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114
114
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contrast_samples = subsets[main_factor].values.flatten.collect{|s| s.split ',' }.flatten.uniq - main_samples
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115
115
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else
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116
116
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contrast_samples = samples - main_samples
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@@ -138,6 +138,6 @@ class Matrix
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138
138
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Misc.mean(v.compact)
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139
139
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end
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140
140
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end
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141
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-
Matrix.new file, labels, value_type,
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141
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+
Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
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142
142
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end
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143
143
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end
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@@ -9,7 +9,7 @@ class Matrix
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9
9
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end
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10
10
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11
11
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name = data_file =~ /:>/ ? File.basename(data_file) : data_file
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12
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-
Persist.persist(name, :tsv, :persist => :update,
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12
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+
Persist.persist(name, :tsv, :persist => :update, :file => path,
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13
13
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:other => {:main => main_samples, :contrast => contrast_samples},
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14
14
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:prefix => "Diff", :dir => Matrix.matrix_dir.differential, :no_load => true) do |file|
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15
15
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@@ -30,7 +30,9 @@ data = rbbt.dm.matrix.differential(#{ R.ruby2R data_file },
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30
30
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log2=#{ R.ruby2R log2 },
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31
31
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outfile = #{R.ruby2R file},
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32
32
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key.field = #{R.ruby2R format},
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33
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-
two.channel = #{R.ruby2R two_channel}
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33
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+
two.channel = #{R.ruby2R two_channel},
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34
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+
namespace = #{R.ruby2R organism}
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35
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+
)
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34
36
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EOS
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35
37
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36
38
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R.run(cmd, :monitor => true)
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-dm
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 1.1.
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4
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+
version: 1.1.14
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Miguel Vazquez
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8
8
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autorequire:
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|
9
9
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bindir: bin
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10
10
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cert_chain: []
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11
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-
date: 2015-
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11
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+
date: 2015-09-18 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: rbbt-util
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