Module: Expression

Extended by:
Workflow
Defined in:
lib/rbbt/expression_old/expression.rb

Class Method Summary collapse

Class Method Details

.average_samples(matrix_file, samples) ⇒ Object 



50
51
52
53
54
55
56
57
58
59
60
61
 
# File 'lib/rbbt/expression_old/expression.rb', line 50

def self.average_samples(matrix_file, samples)
  matrix = TSV.open(matrix_file)
  new = TSV.setup({}, :key_field => matrix.key_field, :fields => matrix.fields, :cast => matrix.cast, :namespace => matrix.namespace)
  positions = samples.collect{|sample| matrix.identify_field sample}.compact
  matrix.with_unnamed do
    matrix.through do |key,values|
      new[key] = Misc.mean(values.values_at(*positions).compact)
    end
  end

  new
end

.barcode(matrix_file, output_file, factor = 3) ⇒ Object 



82
83
84
 
# File 'lib/rbbt/expression_old/expression.rb', line 82

def self.barcode(matrix_file, output_file, factor = 3)
  GE.barcode(matrix_file, output_file, factor)
end

.differential(matrix_file, main, contrast, log2, two_channel) ⇒ Object 



63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
 
# File 'lib/rbbt/expression_old/expression.rb', line 63

def self.differential(matrix_file, main, contrast, log2, two_channel)
  header = TSV.parse_header(Open.open(matrix_file))
  key_field, *fields = header.all_fields
  namespace = header.namespace

  main = main & fields
  contrast = contrast & fields

  if Step === self
    GE.analyze(matrix_file, main, contrast, log2, path, key_field, two_channel)
    TSV.open(path, :type => :list, :cast => :to_f, :namespace => namespace)
  else
    TmpFile.with_file do |path|
      GE.analyze(matrix_file, main, contrast, log2, path, key_field, two_channel)
      TSV.open(path, :type => :list, :cast => :to_f, :namespace => namespace)
    end
  end
end

.load_matrix(data_file, identifier_file, identifier_format, organism) ⇒ Object 



8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
 
# File 'lib/rbbt/expression_old/expression.rb', line 8

def self.load_matrix(data_file, identifier_file, identifier_format, organism)
  log :open_data, "Opening data file"
  data = TSV.open(data_file, :type => :double, :unnamed => true)

  organism ||= data.namespace
 
  if not (identifier_file.nil? or identifier_format.nil? or data.key_field == identifier_format)

    case
    when (fields = (TSV.parse_header(Open.open(identifier_file)).fields) and fields.include?(identifier_format))
      log :attach, "Adding #{ identifier_format } from #{ identifier_file }"
      data = data.attach identifier_file, :fields => [identifier_format]
      log :reorder, "Reordering data fields"
      data = data.reorder identifier_format, data.fields.dup.delete_if{|field| field == identifier_format}
    else
      raise "No organism defined and identifier_format did not match available formats" if organism.nil?
      require 'rbbt/sources/organism'
      organism_identifiers = Organism.identifiers(organism)
      data.identifiers = identifier_file
      log :attach, "Adding #{ identifier_format } from #{ organism_identifiers }"
      data = data.attach organism_identifiers, :fields => [identifier_format]
      log :reorder, "Reordering data fields"
      data = data.reorder identifier_format, data.fields.dup.delete_if{|field| field == identifier_format}
      data
    end

    new_data = TSV.setup({}, :key_field => data.key_field, :fields => data.fields, :type => :list, :cast => :to_f, :namespace => organism, :unnamed => true)
    log :averaging, "Averaging multiple values"
    data.with_unnamed do
      data.through do |key, values|
        new_data[key] = values.collect{|list| Misc.mean(list.collect{|v| v.to_f})}
      end
    end

    data = new_data
  else
    log :ready, "Matrix ready"
  end

  data
end

.top_down(diff_file, cutoff = 0.05) ⇒ Object 



90
91
92
93
94
95
96
97
 
# File 'lib/rbbt/expression_old/expression.rb', line 90

def self.top_down(diff_file, cutoff = 0.05)
  cutoff = -cutoff
  tsv = TSV.open(diff_file, :cast => :to_f).select("adjusted.p.values"){|p| p < 0 and p > cutoff}
  tsv.each do |key,values|
    tsv[key] = values.collect{|v| v.abs}
  end
  tsv
end

.top_up(diff_file, cutoff = 0.05) ⇒ Object 



86
87
88
 
# File 'lib/rbbt/expression_old/expression.rb', line 86

def self.top_up(diff_file, cutoff = 0.05)
  TSV.open(diff_file, :cast => :to_f).select("adjusted.p.values"){|p| p > 0 and p < cutoff}
end