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| author | Christoph Helma <helma@in-silico.ch> | 2016-06-02 19:01:18 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2016-06-02 19:01:18 +0200 |
| commit | 128fd36b2531756c15a93776871e80eb44e524f1 (patch) | |
| tree | ead8f7b83c825d0df8c857866b8d5686d7082927 /lib/nanoparticle.rb | |
| parent | eec5bddbd35c9ecee8021128508d8718bccb4fe3 (diff) | |
proteomics regression validation
Diffstat (limited to 'lib/nanoparticle.rb')
| -rw-r--r-- | lib/nanoparticle.rb | 28 |
1 files changed, 2 insertions, 26 deletions
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb index 3e29ae1..c1bf1b5 100644 --- a/lib/nanoparticle.rb +++ b/lib/nanoparticle.rb @@ -9,10 +9,10 @@ module OpenTox attr_accessor :scaled_values - def physchem_neighbors min_sim: 0.9, dataset_id:, prediction_feature_id: + def physchem_neighbors min_sim: 0.9, dataset_id:, prediction_feature_id:, relevant_features: p name dataset = Dataset.find(dataset_id) - relevant_features = {} + #relevant_features = {} measurements = [] substances = [] # TODO: exclude query activities!!! @@ -24,30 +24,6 @@ module OpenTox end end end - R.assign "tox", measurements - feature_ids = physchem_descriptors.keys.select{|fid| Feature.find(fid).is_a? NumericFeature} - # identify relevant features - feature_ids.each do |feature_id| - feature_values = substances.collect{|s| s["physchem_descriptors"][feature_id].first if s["physchem_descriptors"][feature_id]} - unless feature_values.uniq.size == 1 - R.assign "feature", feature_values - begin - R.eval "cor <- cor.test(tox,feature,method = 'pearson',use='pairwise')" - p_value = R.eval("cor$p.value").to_ruby - if p_value <= 0.05 - r = R.eval("cor$estimate").to_ruby - relevant_features[feature_id] = {} - relevant_features[feature_id]["p_value"] = p_value - relevant_features[feature_id]["r"] = r - relevant_features[feature_id]["mean"] = R.eval("mean(feature, na.rm=TRUE)").to_ruby - relevant_features[feature_id]["sd"] = R.eval("sd(feature, na.rm=TRUE)").to_ruby - end - rescue - warn "Correlation of '#{Feature.find(feature_id).name}' (#{feature_values}) with '#{Feature.find(prediction_feature_id).name}' (#{measurements}) failed." - end - end - end - #p relevant_features.keys.collect{|i| Feature.find(i).name} neighbors = [] substances.each do |substance| values = dataset.values(substance,prediction_feature_id) |