rbbt-dm 1.1.16 → 1.1.17
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- checksums.yaml +4 -4
- data/lib/rbbt/matrix/differential.rb +21 -4
- 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: 02a66fdb598d5f2ebbf7bdbb966e333828c25c74
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4
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+
data.tar.gz: a661e1801711f0de053b622449d0ac201cafef7e
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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: 2dc3a421c78c79619ee01fdaadef01136da9bd6231fa8223be5184e6041e233ed2e8c7643000d055a8c79fe50c93d871fefabaaee625ac8e0bb46d57f2b20b23
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7
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+
data.tar.gz: d48a85fdbd66651cdead6cb3516c20b44f6a3190d95cfb98dad6d00434b114d96457bf7cee58b260fe5facb75ca979d5171569608108c255fdf1ea4dfe2d7a9a
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@@ -18,12 +18,28 @@ class Matrix
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18
18
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19
19
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raise if file.nil?
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20
20
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21
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-
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21
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+
case value_type
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22
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+
when 'two_channel'
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23
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+
log2 = true
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24
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trend = false
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25
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+
two_channel = true
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26
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when nil, 'count', 'counts'
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27
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log2 = true
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28
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+
trend = false
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29
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+
two_channel = false
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30
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+
when 'fpkm'
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31
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log2 = true
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32
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+
trend = true
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33
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two_channel = false
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34
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else
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22
35
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log2 = false
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36
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trend = true
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23
37
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two_channel = false
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24
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-
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38
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+
end
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39
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+
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40
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+
FileUtils.mkdir_p File.dirname(file) unless file.nil? or File.exists? File.dirname(file)
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25
41
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26
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-
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42
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+
cmd = <<-EOS
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27
43
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28
44
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source('#{Rbbt.share.R["MA.R"].find}')
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29
45
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@@ -34,7 +50,8 @@ data = rbbt.dm.matrix.differential(#{ R.ruby2R data_file },
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34
50
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outfile = #{R.ruby2R file},
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35
51
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key.field = #{R.ruby2R format},
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36
52
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two.channel = #{R.ruby2R two_channel},
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37
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-
namespace = #{R.ruby2R organism}
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53
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+
namespace = #{R.ruby2R organism},
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54
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+
eBayes.trend = #{R.ruby2R trend}
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38
55
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)
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39
56
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EOS
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40
57
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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: 1.1.17
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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: 2015-11-13 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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