IsoformExpression.js

IsoformExpression = new Meteor.Collection("isoform_expression");
// ExpressionIsoform = new Meteor.Collection("expression_isoform");

var normalValue = {
  type: Number,
  decimal: true,
  optional: true,
  min: 0,
};

IsoformExpression.attachSchema(new SimpleSchema({
  study_label: { type: String, optional: true },
  collaborations: { type: [String] },
  gene_label: { type: String },
  transcript_label: { type: String }, // should this be isoform_label?
  transcript_version: { type: Number },

  sample_label: { type: String },

  values: {
    type: new SimpleSchema({
      quantile_counts: _.extend({
        label: "Quantile normalized counts",
      }, normalValue),
      quantile_counts_log: _.extend({
        label: "Quantile normalized counts log2",
        max: 100,
        autoValue: function () {
          var quantileCounts = this.siblingField('quantile_counts');
          if (quantileCounts.isSet) {
            return Math.log(quantileCounts.value + 1) / Math.LN2;
          } else {
            this.unset();
          }
        }
      }, normalValue),
      raw_counts: _.extend({
        label: "Raw counts",
      }, normalValue),
      tpm: _.extend({
        label: "TPM (Transcripts Per Million)",
      }, normalValue),
      fpkm: _.extend({
        label: "RPKM (Reads Per Kilobase of transcript per Million mapped reads)",
      }, normalValue),
    }),
    optional: true, // simply because collection2 can't do upserts
  },
}));