Class: GeneConstraintLZ

LocusZoom_Adapters~GeneConstraintLZ()

Retrieve Gene Constraint Data, as fetched from the gnomAD server (or compatible graphQL api endpoint)

This is intended to be the second request in a chain, with special logic that connects it to Genes data already fetched. It assumes that the genes data is returned from the UM API, and thus the logic involves matching on specific assumptions about gene_name format.

Constructor

new GeneConstraintLZ()

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.

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Methods

combineChainBody()

Annotate GENCODE data (from a previous request to the genes adapter) with additional gene constraint data from the gnomAD API. See class description for a summary of how this works.

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getURL()

GraphQL API: request details are encoded in the body, not the URL

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normalizeResponse()

The gnomAD 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.

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