Non-boolean results e.g. percentages

[mathiasbynens]

http://www.snpedia.com/index.php/Gs122/criteria (I’m working on a repo for this one btw) is an example of a genoset for which each criterium has a certain weight that contributes to the end result.

# gs122 looks for increased risk of baldness based on
# 
# rs6625163(A;A) 1.2 (increased risk of baldness)
# rs1160312(A;A) 2 (1.6x increased risk of Male Pattern Baldness.)
# rs1160312(A;G) 2 (1.6x increased risk of Male Pattern Baldness.)
# rs201571(T;T) 2 (more likely to go bald)
# rs6036025(G;G) 1.2 (more likely to go bald)

The number e.g. the 1.2 following rs6625163(A;A) is the magnitude value as provided by SNPedia.

Should there be a way to give each criterium a weight in gql queries? If so, any ideas on what the API should look like? Discuss.

[yocontra]

Naive early morning attempt but here are a few possible APIs, slowly getting sugarier

var test = gql.percentage([
  {test: gql.exact('rs6625163', 'AA'), magnitude: 1.2},
  {test: gql.exact('rs1160312', 'AA'), magnitude: 2},
  {test: gql.exact('rs1160312', 'AG'), magnitude: 2},
  {test: gql.exact('rs201571', 'TT'), magnitude: 2},
  {test: gql.exact('rs6036025', 'GG'), magnitude: 1.2}
]);

test(someDNA); // 85

// gql.magnitude would have to error when being used outside of a percentage
// also kind of breaks the whole "everything is a function" thing
// also magnitude should probably be the second arg here but i was too lazy to change the code
var test = gql.percentage([
  gql.magnify(1.2, gql.exact('rs6625163', 'AA')),
  gql.magnify(2, gql.exact('rs1160312', 'AA')),
  gql.magnify(2, gql.exact('rs1160312', 'AG')),
  gql.magnify(2, gql.exact('rs201571', 'TT')),
  gql.magnify(1.2, gql.exact('rs6036025', 'GG'))
]);

test(someDNA); // 85

// every gql test function would have a magnitude fn that returns a clone of the fn with a new _magnitude property that percentage knows about
// this would allow stuff like gql.percentage([isMale.magnitude(2)])
// but it also limits usage of vanilla functions without wrapping them or adding the _magnitude manually
var test = gql.percentage([
  gql.exact('rs6625163', 'AA').magnitude(1.2),
  gql.exact('rs1160312', 'AA').magnitude(2),
  gql.exact('rs1160312', 'AG').magnitude(2),
  gql.exact('rs201571', 'TT').magnitude(2),
  gql.exact('rs6036025', 'GG').magnitude(1.2)
]);

test(someDNA); // 85

We should think about how this plays into being a part of other queries. If (for example) the isMale module is not a boolean and instead returns a percentage a module that depends on it could do what amounts to gql.and([ifPercentage(isMale, 85), otherStuff...]) but at that point it might be easier/cleaner to just write it out and not have an API for that case

gql.and([
  function(dna){
    return isMale(dna) >= 85;  
  },
  otherStuff...
]);

[mathiasbynens]

API-wise my preference is option 3 (although it could be a bit hairy to implement), then 2.

As a side note, I’d prefer to return actual percentages, e.g. 0.85 over 85.

[yocontra]

With the new update this should be fixed - you can calculate this however you want now, the dna is just an object.