PlinkLDAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the variants plugin. View source.

Example usage#

{
  type: 'LDTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'PlinkLDAdapter',
    uri: 'https://example.com/study.ld',
  },
}

study.ld infers PlinkLDAdapter and LDTrack on its own, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/study.ld',
  assemblyNames: ['hg38'],
}

See the Config slots section below for all available configuration fields.

Adapter for reading pre-computed LD data from a PLINK LD table, either PLINK 2.0's .vcor or PLINK 1.9's .ld. Loads the entire file into memory - suitable for small to medium files.

For large files, use PlinkLDTabixAdapter with tabix indexing.

Expected columns, either spelling: CHR_A BP_A SNP_A CHR_B BP_B SNP_B R2, or plink2's CHROM_A POS_A ID_A CHROM_B POS_B ID_B PHASED_R2 (UNPHASED_R2 for the other statistic). Optional columns: DP / ABS_DPRIME / DPRIME (D'), MAF_A MAF_B / NONMAJ_FREQ_A NONMAJ_FREQ_B. A signed DPRIME is read as its magnitude, which is all a pre-computed cell can be drawn as.

Used by the variant LD display (triangular r² heatmap) and by GWAS Manhattan LD coloring (LocusZoom-style r² to an index SNP). See either guide for generating the table. --r2-phased is the statistic the LD display computes from genotypes, so it is the one whose cells compare with a live triangle.

plink2 --bfile study --r2-unphased --out study

Writes study.vcor, tab-delimited with a commented header:

#CHROM_A	POS_A	ID_A	CHROM_B	POS_B	ID_B	UNPHASED_R2
1	729679	rs4970383	1	752566	rs3131972	0.0925926
1	729679	rs4970383	1	754182	rs3131969	0.157316

PLINK 1.9's plink --bfile study --r2 --out study writes the same table as study.ld, space-padded with a bare header, and loads too.

Related links#

• Track: LDTrack
• Display: LDTrackDisplay
• Guide: GWAS track
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "PlinkLDAdapter", ... }. It also accepts the shorthand keys uri, baseUri in place of writing a location slot out. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.