Class: BioRdf::Parsers::BroadGSEA::ParseResultRecord

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-rdf/parsers/gsea/broadgsea.rb

Overview

Parses a single line result lazily (see features for an example)

GS SIZE SOURCE ES NES NOM-p-val FDR-q-val FWER-p-val Tag% Gene% Signal FDR_(median) glob.p.val

Instance Method Summary collapse

Constructor Details

#initialize(string) ⇒ ParseResultRecord

Returns a new instance of ParseResultRecord.



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 22

def initialize string
  @fields = string.strip.split(/\t/)
end

Instance Method Details

#es ⇒ Object

ES: Enrichment score for the gene set; that is, the degree to which this gene set is overrepresented at the top or bottom of the ranked list of genes in the expression dataset.



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 37

def es
  @es ||= @fields[3].to_f
end

#fdr_q_value ⇒ Object Also known as: fdr

FDR q-value: False discovery rate; that is, the estimated probability that the normalized enrichment score (NES) represents a false positive finding. For example, an FDR of 25% indicates that the result is likely to be valid 3 out of 4 times.



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 56

def fdr_q_value
  @fdr_q_value ||= @fields[6].to_f
end

#fwer_p_value ⇒ Object

FWER p-value: Familywise-error rate; that is, a more conservatively estimated probability that the normalized enrichment score represents a false positive finding. Because the goal of GSEA is to generate hypotheses, the GSEA team recommends focusing on the FDR statistic.



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 65

def fwer_p_value
  @fwer_p_value ||= @fields[7].to_f
end

#geneset_name ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 28

def geneset_name
  @fields[0]
end

#global_p_value ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 74

def global_p_value
  @global_p_value ||= @fields[12].to_f
end

#median_fdr ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 71

def median_fdr
  @median_fdr ||= @fields[11].to_f
end

#nes ⇒ Object

NES: Normalized enrichment score; that is, the enrichment score for the gene set after it has been normalized across analyzed gene sets.



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 42

def nes
  @nes ||= @fields[4].to_f
end

#nominal_p_value ⇒ Object

NOM p-value: Nominal p value; that is, the statistical significance of the enrichment score. The nominal p value is not adjusted for gene set size or multiple hypothesis testing; therefore, it is of limited use in comparing gene sets.



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 49

def nominal_p_value
  @nominal_p_value ||= @fields[5].to_f
end

#signal ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 68

def signal
  @signal ||= @fields[10].to_f
end

#source ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 31

def source
  @fields[2]
end

#to_list ⇒ Object 



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# File 'lib/bio-rdf/parsers/gsea/broadgsea.rb', line 25

def to_list
  @fields
end