blob: 3765842881860521309ced94fb8963c5dee2b11a (
plain)
1
2
3
4
5
6
7
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
|
require 'rserve'
require 'json'
require 'yaml'
require 'csv'
R = Rserve::Connection.new
ENDPOINT = "Cell.association (Net cell association [mL/ug(Mg)])"
def feature_filter
data = JSON.parse(File.read("./data.json"))
features = data["G15.AC"]["physchem"].keys
R.assign "tox", data.collect{|id,cats| cats["tox"][ENDPOINT]}
filtered_features = {}
features.each do |feature|
R.assign "feature", data.collect{|id,cats| cats["physchem"][feature]}
begin
#R.eval "cor <- cor.test(-log(tox),-log(feature),use='complete')"
R.eval "cor <- cor.test(tox,feature,method = 'pearson',use='complete')"
pvalue = R.eval("cor$p.value").to_ruby
if pvalue <= 0.05
r = R.eval("cor$estimate").to_ruby
filtered_features[feature] = {}
filtered_features[feature]["pvalue"] = pvalue
filtered_features[feature]["r"] = r
end
rescue
f = data.collect{|id,cats| cats["physchem"][feature]}
f = R.eval("feature").to_ruby
p f.collect{|f| p f; Math.log f}
p R.eval("log(feature)").to_ruby
end
end
filtered_features.sort{|a,b| a[1]["pvalue"] <=> b[1]["pvalue"]}.to_h
end
puts feature_filter.to_json
|
