Module: TSV
- Defined in:
- lib/rbbt/statistics/random_walk.rb,
lib/rbbt/statistics/rank_product.rb,
lib/rbbt/statistics/hypergeometric.rb
Class Method Summary collapse
- .rank_enrichment(tsv, list, options = {}) ⇒ Object
- .rank_enrichment_for_list(list, hits, options = {}) ⇒ Object
Instance Method Summary collapse
- #annotation_counts(fields = nil, persistence = false, options = {}) ⇒ Object
- #enrichment(list, fields = nil, options = {}) ⇒ Object
- #enrichment_for(tsv, field, options = {}) ⇒ Object
- #rank_enrichment(list, options = {}) ⇒ Object
- #rank_product(fields, reverse = false, &block) ⇒ Object
- #ranks_for(field) ⇒ Object
Class Method Details
.rank_enrichment(tsv, list, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 576 def self.rank_enrichment(tsv, list, = {}) masked = [:masked] if tsv.fields res = TSV.setup({}, :cast => :to_f, :type => :double, :key_field => tsv.key_field, :fields => ["p-value", tsv.fields.first, "Rank"]) else res = TSV.setup({}, :cast => :to_f, :type => :double) end list = list.clean_annotations if list.respond_to? :clean_annotations tsv.with_monitor :desc => "Rank enrichment" do tsv.with_unnamed do tsv.through do |key, values| next if masked and masked.include? key or values.nil? values = values.flatten.compact.reject{|v| v.empty?} matches = (values.respond_to?(:subset) ? values.subset(list) : values & list).compact next if matches.length < 3 list.extend OrderedList unless OrderedList === list total = list.length hits = list.hits(values).collect{|p| p.to_f / total} pvalue = rank_enrichment_for_list(list, values, ) res[key] = [pvalue, matches, hits] end end end FDR.adjust_hash! res, 0 if [:fdr] res end |
.rank_enrichment_for_list(list, hits, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 566 def self.rank_enrichment_for_list(list, hits, = {}) cutoff = [:cutoff] list.extend OrderedList unless OrderedList === list if cutoff list.pvalue(hits, cutoff, ) else list.pvalue(hits, nil, ) end end |
Instance Method Details
#annotation_counts(fields = nil, persistence = false, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/hypergeometric.rb', line 113 def annotation_counts(fields = nil, persistence = false, = {}) fields ||= self.fields fields = [fields] if String === fields or Symbol === fields rename = .delete :rename background = .delete :background field_pos = fields.collect{|f| self.fields.index f}.compact persistence_path = self.respond_to?(:persistence_path)? self.persistence_path : nil Persist.persist(filename, :yaml, :fields => fields, :persist => persistence, :prefix => "Hyp.Geo.Counts", :other => {:background => background, :rename => rename, :persistence_path => persistence_path}) do data ||= {} with_unnamed do case type when :single through :key, field_pos do |key, value| next if background and not background.include?(key) next if value.nil? data[value] ||= [] data[value] << key end when :double through :key, field_pos do |key, values| next if background and not background.include?(key) values.flatten.compact.uniq.each{|value| data[value] ||= []; data[value] << key} end when :list through :key, field_pos do |key, values| next if values.nil? next if background and not background.include?(key) values.compact.uniq.each{|value| data[value] ||= []; data[value] << key} end when :flat through :key, field_pos do |key, values| next if values.nil? next if background and not background.include?(key) values.compact.uniq.each{|value| data[value] ||= []; data[value] << key} end end end if rename Log.debug("Using renames during annotation counts") Hash[*data.keys.zip(data.values.collect{|l| l.collect{|e| rename.include?(e)? rename[e] : e }.uniq.length }).flatten] else Hash[*data.keys.zip(data.values.collect{|l| l.uniq.length}).flatten] end end end |
#enrichment(list, fields = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/hypergeometric.rb', line 164 def enrichment(list, fields = nil, = {}) = Misc.add_defaults , :skip_missing => true, :background => nil background, skip_missing = Misc. , :background, :skip_missing list = list.compact.uniq if Array === background and not background.empty? filter add_filter(:key, background) if defined? AnnotatedArray and AnnotatedArray === list list = list.subset background else list = list & background end end with_unnamed do fields ||= self.fields.first = Misc.add_defaults , :min_support => 3, :fdr => true, :cutoff => false, :add_keys => true add_keys, rename, masked = Misc. , :add_keys, :rename, :masked Log.debug "Enrichment analysis of field #{fields.inspect} for #{list.length} entities" selected = select :key => list.uniq found = selected.keys.length Log.debug "Found #{found} of #{list.length} entities" if skip_missing total = found Log.debug "Using #{ found } as sample size; skipping missing" else total = list.length Log.debug "Using #{ list.length } as sample size" end if background tsv_size = background.length counts = annotation_counts fields, [:persist], :rename => rename, :masked => masked, :background => background else tsv_size = keys.length counts = annotation_counts fields, [:persist], :rename => rename, :masked => masked end annotation_keys = Hash.new selected.with_unnamed do case type when :single selected.through :key, fields do |key, value| value = value.dup annotation_keys[value] ||= [] annotation_keys[value] << key end when :double selected.through :key, fields do |key, values| values.flatten.compact.uniq.reject{|value| value.empty?}.each{|value| value = value.dup annotation_keys[value] ||= [] annotation_keys[value] << key } end when :list selected.through :key, fields do |key, values| values.compact.uniq.reject{|value| value.empty?}.each{|value| value = value.dup annotation_keys[value] ||= [] annotation_keys[value] << key } end when :flat selected.through do |key, values| next if values.nil? values.compact.uniq.reject{|value| value.empty?}.each{|value| value = value.dup annotation_keys[value] ||= [] annotation_keys[value] << key } end end end if Array === background and not background.empty? reset_filters pop_filter end pvalues = {} annotation_keys.each do |annotation, elems| next if masked and masked.include? annotation elems = elems.collect{|elem| rename.include?(elem)? rename[elem] : elem }.compact.uniq if rename count = elems.length next if count < [:min_support] or not counts.include? annotation pvalues[annotation] = Hypergeometric.hypergeometric(count, counts[annotation], tsv_size - counts[annotation], total) end pvalues = FDR.adjust_hash! pvalues if [:fdr] pvalues.delete_if{|k, pvalue| pvalue > [:cutoff] } if [:cutoff] if add_keys tsv = TSV.setup(pvalues.keys.collect{|k| k.dup}, :key_field => fields, :fields => [], :type => :double) tsv.add_field 'p-value' do |annot, values| [pvalues[annot]] end tsv.add_field self.key_field do |annot, values| if list.respond_to? :annotate list.annotate annotation_keys[annot] else annotation_keys[annot] end end tsv else TSV.setup(pvalues, :key_field => fields, :fields => ["p-value"], :cast => :to_f, :type => :single) end end end |
#enrichment_for(tsv, field, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/hypergeometric.rb', line 292 def enrichment_for(tsv, field, = {} ) tsv = tsv.tsv if Path === tsv index = TSV.find_traversal(self, tsv, :in_namespace => false, :persist_input => true) raise "Cannot traverse identifiers" if index.nil? source_keys = index.values_at(*self.keys).flatten.compact.uniq tsv.enrichment source_keys, field, end |
#rank_enrichment(list, options = {}) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 606 def rank_enrichment(list, = {}) TSV.rank_enrichment(self, list, ) end |
#rank_product(fields, reverse = false, &block) ⇒ Object
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# File 'lib/rbbt/statistics/rank_product.rb', line 43 def rank_product(fields, reverse = false, &block) tsv = self.slice(fields) if block_given? scores = fields.collect{|field| tsv.sort_by(field, true, &block)} else scores = fields.collect{|field| tsv.sort_by(field, true){|gene,values| (tsv.type == :single or tsv.type == :list) ? values.to_f : values.flatten.first.to_f}} end positions = {} if reverse size = self.size tsv.keys.each do |entity| positions[entity] = scores.collect{|list| size - list.index(entity)} end else tsv.keys.each do |entity| positions[entity] = scores.collect{|list| list.index(entity) + 1} end end signature_sizes = fields.collect{|field| slice(field).values.select{|v| v and not (v.respond_to?(:empty?) and v.empty?)}.length} score = RankProduct.score(positions, signature_sizes) score end |
#ranks_for(field) ⇒ Object
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# File 'lib/rbbt/statistics/random_walk.rb', line 610 def ranks_for(field) ranks = TSV.setup({}, :key_field => self.key_field, :fields => ["Rank"], :type => :single, :cast => :to_i) sort_by(field, true).each_with_index do |k, i| ranks[k] = i end ranks. = ranks.entity_templates = entity_templates ranks.namespace = namespace ranks end |