Class: LDServer

LocusZoom_Adapters~LDServer()

Fetch linkage disequilibrium information from a UMich LDServer-compatible API, relative to a reference variant. If no plot.state.ldrefvar is explicitly provided, this source will attempt to find the most significant GWAS variant and yse that as the LD reference variant.

THIS ADAPTER EXPECTS TO RECEIVE ASSOCIATION DATA WITH FIELDS variant and log_pvalue. It may not work correctly if this information is not provided.

This source is designed to connect its results to association data, and therefore depends on association data having been loaded by a previous request. For custom association APIs, some additional options might need to be be specified in order to locate the most significant SNP. Variant IDs of the form chrom:pos_ref/alt are preferred, but this source will attempt to harmonize other common data formats into something that the LD server can understand.

Constructor

new LDServer()

Parameters:
Name Type Attributes Default Description
config.url string

The base URL for the remote data.
config.build <optional>
 'GRCh37'

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.
config.source <optional>
 '1000G'

The name of the reference panel to use, as specified in the LD server instance. May be overridden by a global parameter plot.state.ld_source to implement widgets that alter LD display.
config.population <optional>
 'ALL'

The sample population used to calculate LD for a specified source; population names vary depending on the reference panel and how the server was populated wth data. May be overridden by a global parameter plot.state.ld_pop to implement widgets that alter LD display.
config.method <optional>
 'rsquare'

The metric used to calculate LD
Source:
See: