intervalFrequencies

This service provides access to binned CNV frequency information of data "collations" in the Progenetix project databases. A typical use would be the retrieval of data for a single collation, e.g. by its identifier (e.g. NCIT:C7376, PMID:22824167, pgx:cohort-TCGAcancers).

Response

Results are provides in a modified JSON Beacon v2 response, inside the results array. Each frequency set is provided as object, with the single bin frequencies in interval_frequencies.

For the usual "single frequency set" use case this would result in a possible direct access to the frequecy list at response.results[0].interval_frequencies.

{
  "meta": {
    ...
  },
  "responseSummary": {
    "exists": true,
    "numTotalResults": 1,
  },
  "response": {
    "results": [
      {
        "datasetId": "progenetix",
        "frequencymapSamples": 267,
        "groupId": "NCIT:C7376",
        "intervalFrequencies": [
          {
              "arm": "p",
              "cytobands": "1p36.33",
              "end": 400000,
              "gainFrequency": 3.371,
              "gainHlfrequency": 0.0,
              "id": "1p:0-400000",
              "lossFrequency": 5.618,
              "lossHlfrequency": 0.0,
              "no": 1,
              "referenceName": "1",
              "size": 400000,
              "start": 0
          },
          {
              "arm": "p",
              "cytobands": "1p36.33",
              "end": 1400000,
              "gainFrequency": 5.618,
              "gainHlfrequency": 0.375,
              "id": "1p:400000-1400000",
              "lossFrequency": 10.861,
              "lossHlfrequency": 0.0,
              "no": 2,
              "referenceName": "1",
              "size": 1000000,
              "start": 400000
          },

Parameters

id

• standard parameter to retrieve a frequency set by its id
• available values can be looked up using the collations service:
• progenetix.org/services/collations?method=ids&filters=NCIT&datasetIds=progenetix
• an id value will override any given filters

filters

• a single or a comma-concatenated list of identifiers

intervalType

• not implemented
• default use is 1Mb, i.e. megabase binning (with diverging size for each chromosome's q-terminal interval)

output

The output parameter here can set set autput format. Options are:

• not set ...
• standard JSON response
• output=pgxseg
• Proggenetix .pgxseg columnar format, with a line for each interval and gain, loss frequencies
• output=pgxmatrix
• Progenetix .pgxmatrix matrix format, with a line for each frequency set and interval frequencies provided in the columns (i.e. usually first all gain frequencies, then all loss frequencies)
• makes sense for multiple frequency sets, e.g. for clustering

Examples

• progenetix.org/services/intervalFrequencies/?id=pgx:cohort-TCGAcancers
• progenetix.org/services/intervalFrequencies/?filters=NCIT:C7376,PMID:22824167
• progenetix.org/services/intervalFrequencies/?output=pgxseg&filters=NCIT:C7376,PMID:22824167
• progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C7376,PMID:22824167