# PlinkLDAdapter

Auto-generated config schema for the current JBrowse release — see the
[config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the `variants`
plugin.
[View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/PlinkLDAdapter/configSchema.ts).

## Example usage

```js
{
  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](https://jbrowse.org/jb2-staging/docs/config_guides/tracks#the-shortest-track).

```js
{
  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](https://jbrowse.org/jb2-staging/docs/config_guides/variant_track#linkage-disequilibrium-ld-display)
(triangular r² heatmap) and by
[GWAS Manhattan LD coloring](https://jbrowse.org/jb2-staging/docs/config_guides/gwas_track#preparing-the-ld-file)
(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.

```bash
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](../ldtrack)
- **Display:** [LDTrackDisplay](../ldtrackdisplay)

## Config slots

These slots go inside the track's `adapter`:
`"adapter": { "type": "PlinkLDAdapter", ... }`. It also accepts the
[shorthand](https://jbrowse.org/jb2-staging/docs/config_guides/file_types#the-uri-shorthand) keys `uri`,
`baseUri` in place of writing a location slot out. Slot types (`fileLocation`,
`frozen`, ...) are explained in the
[config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types). Slots a base
configuration contributes are listed here too, so this table is the whole
surface.

<!-- prettier-ignore -->
| Slot | Description |
| --- | --- |
| <span id="slot-ldlocation">**ldLocation**</span><br>[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = <code>{ uri: '/path/to/plink.ld', locationType: 'UriLocation' }</code> | Location of the PLINK LD table (.ld, .ld.gz or .vcor) |