Class: GeneLZ

LocusZoom_Adapters~GeneLZ()

Retrieve Gene Data, as fetched from the LocusZoom/Portaldev API server (or compatible format)

Constructor

new GeneLZ()

Parameters:
Name Type Description
config.url string

The base URL for the remote data

config.params Object
Properties
Name Type Attributes Description
build <optional>

The genome build to use when calculating LD relative to a specified reference variant. May be overridden by a global parameter plot.state.genome_build so that all datasets can be fetched for the appropriate build in a consistent way.

source Number <optional>

The ID of the chosen gene dataset. Most usages should omit this parameter and let LocusZoom choose the newest available dataset to use based on the genome build: defaults to recent GENCODE data, GRCh37.

Source:
See:

Methods

extractFields()

Does not attempt to namespace or modify the fields from the API payload; the payload format is very complex and quite coupled with the data rendering implementation. Typically, requests to this adapter specify a single dummy field sufficient to trigger the request: fields:[ 'gene:all' ]

Source:

getURL()

Add query parameters to the URL to construct a query for the specified region

Source:

normalizeResponse(data) → {Array.<Object>|Object}

The UM genes API has a very complex internal data format. Bypass any record parsing, and provide the data layer with the exact information returned by the API. (ignoring the fields array in the layout)

Parameters:
Name Type Description
data
Source:
Returns:
Type
Array.<Object> | Object