Services: 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, pgxcohort-TCGAcancers).


Contents


Identify existing collations for frequency maps retrieval

The complete set of all collation codes can be retrieved through

id  label count w/ children direct count
NCIT:C3262	Neoplasm	116232	0
NCIT:C156482	Genitourinary System Neoplasm	16410	0
NCIT:C4893	Benign Urinary System Neoplasm	93	0
NCIT:C159209	Kidney Leiomyoma	1	1
NCIT:C4526	Kidney Oncocytoma	85	85
...

Response Types

Download .pgxseg files

.pgxseg files are tab-delimited, columnar text files where each line provides information about features or measurements associated with a genomic region. More information can be found on the file formats page.

Stream JSON data

JSON formatting is provided in a Beacon v2 response, inside the results array. Each frequency set is provided as object, with the single bin frequencies in interval_frequencies. For more information see the beaconresponse json documentation.

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

{
  "meta": {
    ...
  },
  "response": {
    "error": {
      "error_code": 200,
      "error_message": ""
    },
    "exists": true,
    "numTotalResults": 1,
    "results": [
      {
        "datasetId": "progenetix",
        "id": "pgxcohort-TCGAcancers",
        "intervalFrequencies": [
          {
            "referenceName": "1",
            "end": 1000000,
            "gainFrequency": 0,
            "index": 0,
            "lossFrequency": 0,
            "start": 0
          },
          {
            "referenceName": "1",
            "end": 2000000,
            "gainFrequency": 0,
            "index": 1,
            "lossFrequency": 0,
            "start": 1000000
          },

Parameters

id

filters

intervalType

method

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

Examples

2021-05-06
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