2a:null 2b:["$","title",null,{"children":"PLCO SDK | Erika Nemeth | Observable"}] 30:[] 2e:{"id":"b238d7cb4c1c7dbf","slug":"plco-sdk","title":"PLCO SDK","thumbnail":"5976ca9cad5384620d94bbbcc2a17066e353dd04ef0507db6e05f2fe14e5935b","access_level":"public","create_time":"$D2021-06-02T16:51:34.315Z","update_time":"$D2021-06-10T19:27:49.445Z","view_time":null,"first_public_time":"$D2021-06-09T19:49:28.058Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"be31c14f0c46ba8e","login":"enemeth19","name":"Erika Nemeth","avatar_url":"https://avatars-next.observableusercontent.com/4b8ec923a78002d01c443682ba0a0b90eeab2fb7f884a3e506bed247453915a9","tier":"starter_2024"},"version":201,"publish_version":201,"role":null,"authored":false,"authors":[{"type":"individual","id":"9887bbe532a2fe8d","login":"enemeth19","name":"Erika Nemeth","avatar_url":"https://avatars-next.observableusercontent.com/4b8ec923a78002d01c443682ba0a0b90eeab2fb7f884a3e506bed247453915a9","tier":null}],"members":[{"type":"individual","id":"9887bbe532a2fe8d","login":"enemeth19","name":"Erika Nemeth","avatar_url":"https://avatars-next.observableusercontent.com/4b8ec923a78002d01c443682ba0a0b90eeab2fb7f884a3e506bed247453915a9","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"PLCO SDK","cells":[{"id":0,"value":"html`\n

PLCO SDK

\nA notebook to accompany our development of an SDK for usage of the PLCO API\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":100,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":45,"value":"html`\n

Step 1: Load SDK

First, let's load plco.js, a JS file contained in our GitHub repo

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":28,"value":"plco = require('https://episphere.github.io/plco/plco.js')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":159,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":137,"value":"html`\n

Step 2: Check if API service is available

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":93,"value":"html`\n

ping

\nRetrieve status of API service\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":14,"value":"await plco.api.ping()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":151,"value":"html`\n

If response is \"true\", then we may proceed in using the SDK to retrieve data from the PLCO API

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":162,"value":"html`\n

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":155,"value":"html`\n

Step 3: Browse data via the PLCO API

Example values are passed as arguments to each function below

Note: Any bolded blue text indicates an API endpoint term

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":82,"value":"html`\n

download

\nDownload the original association results for a phenotype\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":131,"value":"//await plco.api.download(\"phenotype_id:3080\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":165,"value":"html`\n

metadata

\nRetrieve metadata about each phenotype specified\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":168,"value":"await plco.api.metadata({ phenotype_id: 3080, sex: \"female\", ancestry: \"european\" })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":173,"value":"html`\n

participants

\nRetrieve single phenotype's aggregated participant data\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":176,"value":"await plco.api.participants({phenotype_id: 2250})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":180,"value":"html`\n

summary

\nRetrieves variants for all chromosomes at a resolution of 400x800 bins across the entire genome and -log10(p) range. Each bin can contain multiple variants.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":185,"value":"await plco.api.summary({ phenotype_id: 3080, sex: \"female\", ancestry: \"european\", p_value_nlog_min: 4 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":187,"value":"html`\n

variants

\nRetrieves a list of variants by phenotype ID\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":200,"value":"await plco.api.variants({ phenotype_id: 3080, sex: \"female\", ancestry: \"european\", chromosome: 8, p_value_nlog_min: 4, limit: 10 })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":79,"value":"html`\n

Some helper functions

\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":70,"value":"await plco.api.get(\"metadata?phenotype_id=3080\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":73,"value":"await plco.api.parms2string()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2f:"$2e:body"