JSDoc: Namespace: api

Sub-module grouping API methods.

Properties:

Name	Type	Description
`download`	function	`plco.api.download`
`metadata`	function	`plco.api.metadata`
`participants`	function	`plco.api.participants`
`pca`	function	`plco.api.pca`
`phenotypes`	function	`plco.api.phenotypes`
`points`	function	`plco.api.points`
`summary`	function	`plco.api.summary`
`variants`	function	`plco.api.variants`
`ping`	function	`plco.api.ping`

Source:

plco.js, line 461

Methods

(static) download(parms, phenotype_idopt, get_link_onlyopt)

Downloads the original association results in tsv.gz format.

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	integer	<optional>	3080	A numeric phenotype id.
`get_link_only`	string	<optional>		Optional. If set to 'true', returns the download link instead of redirecting automatically to the file.

Source:

plco.js, line 533

Returns:

Results of the API call.

(static) metadata(parms, phenotype_idopt, sexopt, ancestryopt, rawopt)

Retrieves metadata for phenotypes specified

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	number	<optional>	3080	A phenotype id.
`sex`	string	<optional>	female	A sex, which may be "all", "female", or "male".
`ancestry`	string	<optional>	european	A character vector specifying ancestries to retrieve data for.
`raw`	string	<optional>		Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 566

Returns:

A dataframe containing phenotype metadata

Example

plco.api.metadata()
plco.api.metadata({ phenotype_id: 3080, sex: "female", ancestry: "european" })
plco.api.metadata("phenotype_id=3080&sex=female&ancestry=european")
plco.api.metadata([["phenotype_id",3080], ["sex","female"], ["ancestry","european"]])
plco.api.metadata({}, 3080, "female", "european")

(static) participants(parms, phenotype_idopt, columnsopt, precisionopt, rawopt)

Retrieves aggregate counts for participants. Aggregate counts under 10 are returned as "< 10".

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	integer	<optional>	2250	A numeric phenotype id.
`columns`	string	<optional>		Optional. A character vector specifying properties for which to retrieve counts for. Valid properties are: value, ancestry, genetic_ancestry, sex, and age.
`precision`	integer	<optional>		Optional. For continuous phenotypes, a numeric value specifying the -log10(precision) to which values should be rounded to.
`raw`	string	<optional>		Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 599

Returns:

Results of the API call.

(static) pca(parms, phenotype_idopt, platformopt, pc_xopt, pc_yopt, limitopt, rawopt)

Retrieve PCA coordinates for the specified phenotype and platform.

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	integer	<optional>	3080	A numeric phenotype id.
`platform`	string	<optional>	PLCO_GSA	A character vector specifying the platform to retrieve data for.
`pc_x`	integer	<optional>	1	A numeric value (1-20) specifying the x axis's principal component.
`pc_y`	integer	<optional>	2	A numeric value (1-20) specifying the y axis's principal component.
`limit`	integer	<optional>		Optional. A numeric value to limit the number of variants returned (used for pagination). Capped at 1 million.
`raw`	string	<optional>		Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 640

Returns:

A dataframe containing pca coordinates.

Example

plco.api.pca()
plco.api.pca({}, 3080, 'PLCO_GSA', 1, 1, 1000)
plco.api.pca({phenotype_id: 3080, platform: 'PLCO_GSA', pc_x: 1, pc_y: 1, limit: 1000 })
plco.api.pca("phenotype_id=3080&platform=PLCO_GSA&pc_x=1&pc_y=1&limit=1000")
plco.api.pca([["phenotype_id",3080], ["platform","PLCO_GSA"], ["pc_x",1], ["pc_y",1], ["limit",1000]])

(static) phenotypes(parms, qopt, rawopt)

Retrieves phenotypes

Parameters:

Name	Type	Attributes	Description
`parms`	object \| string \| Array.<Array>		A JSON object, query string, or 2-d array containing the query parameters.
`q`	string	<optional>	Optional. A query term
`raw`	string	<optional>	Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 686

Returns:

If query is specified, a list of phenotypes that contain the query term is returned. Otherwise, a tree of all phenotypes is returned.

Example

plco.api.phenotypes()
plco.api.phenotypes({ q: "first_ca125_level" })
plco.api.phenotypes("q=first_ca125_level")
plco.api.phenotypes([["q","first_ca125_level"]])
plco.api.phenotypes({}, "first_ca125_level")

(static) ping()

Returns the status of the PLCO API.

Source:

plco.js, line 482

(static) points(parms, phenotype_idopt, sexopt, ancestryopt, rawopt)

Retrieves sampled variants suitable for visualizing a QQ plot for the specified phenotype, sex, and ancestry.

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	integer	<optional>	3080	A numeric phenotype id.
`sex`	string	<optional>	female	A character vector specifying a sex to retrieve data for.
`ancestry`	string	<optional>	european	A character vector specifying ancestries to retrieve data for.
`raw`	string	<optional>		Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 712

Returns:

A dataframe containing variants.

(static) summary(parms, phenotype_idopt, sexopt, ancestryopt, p_value_nlog_minopt, rawopt)

Retrieve variants for all chromosomes at a resolution of 400x800 bins across the whole genome and specified -log10(p) range

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	number	<optional>	3080	A phenotype id.
`sex`	string	<optional>	female	A sex, which may be "all", "female", or "male".
`ancestry`	string	<optional>	european	A character vector specifying ancestries to retrieve data for.
`p_value_nlog_min`	number	<optional>	4	A numeric value >= 0 specifying the minimum -log10(p) for variants.
`raw`	string	<optional>		Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 751

Returns:

A dataframe with aggregated variants.

Example

plco.api.summary()
plco.api.summary({ phenotype_id: 3080, sex: "female", ancestry: "european", p_value_nlog_min: 4 })
plco.api.summary("phenotype_id=3080&sex=female&ancestry=european&p_value_nlog_min=4")
plco.api.summary([["phenotype_id",3080], ["sex","female"], ["ancestry","european"], ["p_value_nlog_min",4]])
plco.api.summary({}, 3080, "female", "european", 4)

(static) variants(parms, phenotype_idopt, sexopt, ancestryopt, chromosomeopt, columnsopt, snpopt, positionopt, position_minopt, position_maxopt, p_value_nlog_minopt, p_value_nlog_maxopt, p_value_minopt, p_value_maxopt, orderByopt, orderopt, offsetopt, limitopt, rawopt)

Retrieve variants for specified phenotype, sex, ancestry, chromosome, and other optional fields.

Parameters:

Name	Type	Attributes	Default	Description
`parms`	object \| string \| Array.<Array>			A JSON object, query string, or 2-d array containing the query parameters.
`phenotype_id`	number	<optional>	3080	Phenotype id(s)
`sex`	string	<optional>	female	A sex, which may be "all", "female", or "male".
`ancestry`	string	<optional>	european	An ancestry, which may be "african_american", "east_asian", or "european".
`chromosome`	number	<optional>	8	A chromosome number.
`columns`	string	<optional>		Optional Properties for each variant. Default: all properties.
`snp`	string	<optional>		Optional Snps.
`position`	number	<optional>		Optional The exact position of the variant within a chromosome.
`position_min`	number	<optional>		Optional The minimum chromosome position for variants.
`position_max`	number	<optional>		Optional The maximum chromosome position for variants.
`p_value_nlog_min`	number	<optional>		Optional The minimum -log10(p) of variants in the chromosome.
`p_value_nlog_max`	number	<optional>		Optional The maximum -log10(p) of variants in the chromosome.
`p_value_min`	number	<optional>		Optional The minimum p-value of variants in the chromosome.
`p_value_max`	number	<optional>		Optional The maximum p-value of variants in the chromosome.
`orderBy`	string	<optional>		Optional A property to order variants by. May be "id", "snp", "chromosome", "position", "p_value", or "p_value_nlog".
`order`	string	<optional>		Optional An order in which to sort variants. May be "asc" or "desc".
`offset`	number	<optional>		Optional The number of records by which to offset the variants (for pagination)
`limit`	number	<optional>		Optional The maximum number of variants to return (for pagination). Highest allowed value is 1 million.
`raw`	string	<optional>		Optional. If true, returns data in an array of arrays instead of an array of objects.

Source:

plco.js, line 804

Returns:

A dataframe with variants.

Example

plco.api.variants()
plco.api.variants({ phenotype_id: 3080, sex: "female", ancestry: "european", chromosome: 8, limit: 10 })
plco.api.variants("phenotype_id=3080&sex=female&ancestry=european&chromosome=8&limit=10")
plco.api.variants([["phenotype_id",3080], ["sex","female"], ["ancestry","european"], ["chromosome",8], ["limit",10]])
plco.api.variants({}, 3080, "female", "european", 8)