Module: ext/lz-parsers

Optional LocusZoom extension: must be included separately, and after LocusZoom has been loaded

This plugin exports helper function, as well as a few optional extra helpers for rendering the plot. The GWAS parsers can be used without registering the plugin.

To use in an environment without special JS build tooling, simply load the extension file as JS from a CDN (after any dependencies):

<script src="https://cdn.jsdelivr.net/npm/locuszoom@INSERT_VERSION_HERE/dist/ext/lz-parsers.min.js" type="application/javascript"></script>

To use with ES6 modules, import the helper functions and use them with your layout:

import { install, makeGWASParser, makeBed12Parser, makePlinkLDParser } from 'locuszoom/esm/ext/lz-parsers';
LocusZoom.use(install);

Features provided

Source:

Methods

(inner) makeBed12Parser(options)

Parse a BED file, according to the widely used UCSC (quasi-)specification

NOTE: This original version is aimed at tabix region queries, and carries an implicit assumption that data is the only thing that will be parsed. It makes no attempt to identify or handle header rows / metadata fields.

Parameters:
Name Type Description
options object
Properties
Name Type Description
normalize Boolean

Whether to normalize the output to the format expected by LocusZoom (eg type coercion for numbers, removing chr chromosome prefixes, and using 1-based and inclusive coordinates instead of 0-based disjoint intervals)
Source:
Returns:

function A configured parser function that runs on one line of text from an input file

(inner) makeGWASParser(options) → {function}

Specify how to parse a GWAS file, given certain column information. Outputs an object with fields in portal API format.

All column options must be provided as 1-indexed column IDs (human-friendly argument values)

Parameters:
Name Type Description
options
Properties
Name Type Attributes Default Description
marker_col <optional>

A single identifier that specifies all of chrom, pos, ref, and alt as a single string field. Eg 1:23_A/C
chrom_col <optional>

Chromosome
pos_col <optional>

Position
ref_col <optional>

Reference allele (relative to human reference genome, eg GRCh37 or 38).
alt_col <optional>

Alt allele. Some programs specify generic A1/A2 instead; it is the job of the user to identify which columns of this GWAS are ref and alt.
rsid_col <optional>

rsID
pvalue_col

p-value (or -log10p)
beta_col <optional>
stderr_beta_col <optional>
allele_freq_col <optional>

Specify allele frequencies directly
allele_count_col <optional>

Specify allele frequencies in terms of count and n_samples
n_samples_col <optional>
is_alt_effect <optional>
 true

Some programs specify beta and frequency information in terms of ref, others alt. Identify effect allele to orient values to the correct allele.
is_neg_log_pvalue <optional>
 false
delimiter <optional>
 '\t'

Since this parser is usually used with tabix data, this is rarely changed (tabix does not accept other delimiters)
Source:
Returns:

A parser function that can be called on each line of text with the provided options

Type
function

(inner) makePlinkLdParser(options) → {function}

Parse the output of plink v1.9 R2 calculations relative to one (or a few) target SNPs. See: https://www.cog-genomics.org/plink/1.9/ld and reformatting commands at https://www.cog-genomics.org/plink/1.9/other

Parameters:
Name Type Description
options object
Properties
Name Type Attributes Default Description
normalize boolean <optional>
 true

Normalize fields to expected datatypes and format; if false, returns raw strings as given in the file
Source:
Returns:

A configured parser function that runs on one line of text from an input file

Type
function