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# File 'lib/rbbt/matrix/differential.rb', line 4
def differential(main, contrast, path = nil)
all_samples = self.samples
if Array === main and Array === contrast
main_samples, contrast_samples = main, contrast
else
main_samples, contrast_samples = comparison main, contrast
end
name = data_file =~ /:>/ ? File.basename(data_file) : data_file
main_samples = main_samples & all_samples
contrast_samples = contrast_samples & all_samples
raise "No main samples found" if main_samples.empty?
raise "No contrast samples found" if contrast_samples.empty?
Persist.persist(name, :tsv, :persist => true, :file => path,
:other => {:main => main_samples, :contrast => contrast_samples},
:prefix => "Diff", :dir => Matrix.matrix_dir.differential, :no_load => true) do |file|
raise if file.nil?
case value_type
when 'two_channel'
log2 = true
trend = false
two_channel = true
when nil, 'count', 'counts'
log2 = true
trend = false
two_channel = false
when 'fpkm'
log2 = true
trend = true
two_channel = false
when 'log2 ratio', 'transformed count'
log2 = false
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
source('#{Rbbt.share.R["MA.R"].find(:lib)}')
data = rbbt.dm.matrix.differential(#{ R.ruby2R data_file },
main = #{R.ruby2R(main_samples)},
contrast = #{R.ruby2R(contrast_samples)},
log2=#{ R.ruby2R log2 },
outfile = #{R.ruby2R file},
key.field = #{R.ruby2R format},
two.channel = #{R.ruby2R two_channel},
namespace = #{R.ruby2R organism},
eBayes.trend = #{R.ruby2R trend}
)
EOS
R.run(cmd, :monitor => true)
end
end
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