Global - Documentation

Members

(constant) readObjectRegistry :object

Description:

Registry of reader functions. Each key is a takane object type, and each value is a function that accepts the same arguments as readObject.

Source:

general.js, line 30

Registry of reader functions. Each key is a takane object type, and each value is a function that accepts the same arguments as readObject.

Type:

object

(constant) saveObjectRegistry :Array

Description:

Registry of saving functions. Each entry should be an array of length 2, containing a Javascript class and its saving function. Each saving function should accept the same arguments as saveObject. Subclasses should be placed after their parents in this array.

Source:

general.js, line 83

Registry of saving functions. Each entry should be an array of length 2, containing a Javascript class and its saving function. Each saving function should accept the same arguments as saveObject. Subclasses should be placed after their parents in this array.

Type:

Array

Methods

joinPath(args)

Description:

Join paths while accounting for . inputs.

Source:

utils.js, line 9

Parameters:

Name	Type	Description
`args`	string	One or more strings containing path components. These should not have leading or trailing `/` but may be equal to `.`

Returns:

The joined path.

(async) readDataFrame(path, metadata, globals, optionsopt) → {external:DataFrame}

Source:

DataFrame.js, line 31

Parameters:

Name Type Attributes Default Description

path

string

Path to the takane-formatted object directory containing the DataFrame.

metadata

object

Takane object metadata, typically generated by calling readObjectFile on path.

globals

object

Object satisfying the GlobalsInterface.

options

object

{}

Further options.

Properties

Name	Type	Attributes	Default	Description
`DataFrame_readNested`	function \| boolean	<optional>	`true`	How to read columns containing nested objects. If `true`, `readObject` is used, while if `false`, nested objects will be skipped. If a function is provided, it should accept `nrow` (the number of rows in the data frame) as well as `path`, `metadata`, `globals` and `options` (as described above); and should return an object (possibly asynchronously) for which `NUMBER_OF_ROWS` is equal to `nrow`.
`DataFrame_readMetadata`	function \| boolean	<optional>	`true`	How to read the metadata. If `true`, `readObject` is used, while if `false`, metadata will be skipped. If a function is provided, it should accept `path`, `metadata`, `globals` and `options` (as described above), and return a List.
`DataFrame_toTypedArray`	boolean	<optional>	`false`	Whether to report integer/number vectors without missing values as TypedArrays. If `false`, vectors are reported as instances of an appropriately-typed List subclass.

Returns:

The data frame.

Type: external:DataFrame

(async) readList(path, metadata, globals, optionsopt) → {external:List}

Source:

List.js, line 115

Parameters:

Name Type Attributes Default Description

path

string

Path to the takane-formatted object directory containing the List.

metadata

object

Takane object metadata, typically generated by calling readObjectFile on path.

globals

object

Object satisfying the GlobalsInterface.

options

object

{}

Further options.

Properties

Name	Type	Attributes	Default	Description
`List_toScalar`	boolean	<optional>	`false`	Whether to report unnamed scalars as Javascript scalars. Integers are automatically converted to floating-point. If `false`, scalars are reported as instances of an appropriately-typed List subclass with length 1 and a `_jaspalite_scalar` property.
`List_toTypedArray`	boolean	<optional>	`false`	Whether to report unnamed integer/number vectors without missing values as TypedArrays. If `false`, such vectors are reported as instances of an appropriately-typed List subclass.

Returns:

The list.

Type: external:List

(async) readObject(path, metadatanullable, globals, optionsopt)

Description:

This function will inspect readObjectRegistry to check if any reader function is supplied for the takane object type at path. If found, it will use that function, otherwise it will fall back to the default functions:
- readDataFrame, to read DataFrame objects.
- readSummarizedExperiment, to read SummarizedExperiment objects.
- readRangedSummarizedExperiment, to read RangedSummarizedExperiment objects.
- readSingleCellExperiment, to read SingleCellExperiment objects.

Source:

general.js, line 50

Parameters:

Name	Type	Attributes	Default	Description
`path`	string			Path to a takane-formatted object directory.
`metadata`	object	<nullable>		Object metadata. If `null`, this is automatically loaded by calling `readObjectFile` on `path`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options, to be passed to the reader functions for individual takane object types.

Returns:

Some in-memory representation of the takane object at path.

(async) readObjectFile(path, globals) → {object}

Source:

general.js, line 15

Parameters:

Name	Type	Description
`path`	string	Path to the takane-formatted object directory containing the DataFrame.
`globals`	object	Object satisfying the GlobalsInterface.

Returns:

Object metadata.

Type: object

(async) readRangedSummarizedExperiment(path, metadata, globals, optionsopt) → {external:RangedSummarizedExperiment}

Source:

RangedSummarizedExperiment.js, line 22

Parameters:

Name	Type	Attributes	Default	Description
`path`	string			Path to the takane-formatted object directory containing the RangedSummarizedExperiment.
`metadata`	object			Takane object metadata, typically generated by calling `readObjectFile` on `path`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options, see also readSummarizedExperiment.

Returns:

The ranged summarized experiment object.

Type: external:RangedSummarizedExperiment

(async) readSingleCellExperiment(path, metadata, globals, optionsopt) → {external:SingleCellExperiment}

Source:

SingleCellExperiment.js, line 31

Parameters:

Name Type Attributes Default Description

path

string

Path to the takane-formatted object directory containing the SingleCellExperiment.

metadata

object

Takane object metadata, typically generated by calling readObjectFile on path.

globals

object

Object satisfying the GlobalsInterface.

options

object

{}

Further options.

Properties

Name	Type	Attributes	Default	Description
`SingleCellExperiment_readReducedDimension`	function \| boolean	<optional>	`true`	How to read each dimensionality reduction result. If `true`, `readObject` is used, while if `false`, the reduced dimensions will be skipped. If a function is provided, it should accept `ncol` (the number of columns in the SingleCellExperiment) as well as `path`, `metadata`, `globals` and `options` (as described above); and should return an object (possibly asynchronously) for which `NUMBER_OF_ROWS` is equal to `ncol`.
`SingleCellExperiment_readAlternativeExperiment`	function \| boolean	<optional>	`true`	How to read each alternative experiment. If `true`, `readObject` is used, while if `false`, the alternative experiments will be skipped. If a function is provided, it should accept `ncol` (the number of columns in the SingleCellExperiment) as well as `path`, `metadata`, `globals` and `options` (as described above); and should return a SummarizedExperiment (possibly asynchronously) for which `NUMBER_OF_COLUMNS` is equal to `ncol`.

Returns:

The single-cell experiment object.

Type: external:SingleCellExperiment

(async) readSummarizedExperiment(path, metadata, globals, optionsopt) → {external:SummarizedExperiment}

Source:

SummarizedExperiment.js, line 30

Parameters:

Name Type Attributes Default Description

path

string

Path to the takane-formatted object directory containing the SummarizedExperiment.

metadata

object

Takane object metadata, typically generated by calling readObjectFile on path.

globals

object

Object satisfying the GlobalsInterface.

options

object

{}

Further options.

Properties

Name	Type	Attributes	Default	Description
`SummarizedExperiment_readAssay`	function	<optional> <nullable>	`null`	How to read the assays. If `null`, `readObject` is used. If a function is provided, it should accept `nrow` and `ncol` (the number of rows and columns in the SummarizedExperiment, respectively) as well as `path`, `metadata`, `globals` and `options` (as described above); and should return an object (possibly asynchronously) for which `NUMBER_OF_ROWS` is equal to `nrow` and `NUMBER_OF_COLUMNS` is equal to `ncol`.
`SummarizedExperiment_readMetadata`	function \| boolean	<optional>	`true`	How to read the metadata. If `true`, `readObject` is used, while if `false`, metadata will be skipped. If a function is provided, it should accept `path`, `metadata`, `globals` and `options` (as described above), and return a List.

Returns:

The summarized experiment object.

Type: external:SummarizedExperiment

(async) saveDataFrame(x, path, globals, optionsopt)

Source:

DataFrame.js, line 288

Parameters:

Name	Type	Attributes	Default	Description
`x`	external:DataFrame			The data frame.
`path`	string			Path to the directory in which to save `x`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options.
`?options.DataFrame_saveOther`	function	<optional>	`null`	Function to save custom class instances as columns of a data frame, without resorting to a reference to an external object. This should accept `y`, an instance of a custom object; `handle`, the H5Group in which `y` is to be saved; and `name`, the name of the child of `handle` in which to save `y`. It should return `true` if `y` was saved and `false` otherwise (e.g., if it does not know how to handle the class of`y`).

Returns:

x is stored at path.

(async) saveList(x, path, globals, optionsopt)

Source:

List.js, line 290

Parameters:

Name	Type	Attributes	Default	Description
`x`	external:List			The list.
`path`	string			Path to the directory in which to save `x`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options.
`?options.List_saveOther`	function	<optional>	`null`	Function to save custom class instances within a list, without resorting to a reference to an external object. This should accept `y`, an instance of a custom object, and return an object containing the contents of `y` in the uzuki2 JSON format. If the class of `y` is not supported, `null` should be returned instead.

Returns:

x is stored at path.

(async) saveObject(x, path, globals, optionsopt)

Description:

This function will inspect saveObjectRegistry to check if any saving function is supplied for x. If found, it will use that function, otherwise it will fall back to the default functions:
- saveDataFrame, to save DataFrame objects.
- saveSummarizedExperiment, to save SummarizedExperiment objects.
- saveRangedSummarizedExperiment, to save RangedSummarizedExperiment objects.
- saveSingleCellExperiment, to save SingleCellExperiment objects.

Source:

general.js, line 102

Parameters:

Name	Type	Attributes	Default	Description
`x`	Any			The takane-compatible object to be saved.
`path`	string			Path to the directory in which to save `x`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options.

Returns:

x is stored at path.

(async) saveRangedSummarizedExperiment(x, path, globals, optionsopt)

Source:

RangedSummarizedExperiment.js, line 50

Parameters:

Name	Type	Attributes	Default	Description
`x`	external:RangedSummarizedExperiment			The ranged summarized experiment.
`path`	string			Path to the directory in which to save `x`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options, see also `saveSummarizedExperiment`.

Returns:

x is stored at path.

(async) saveSingleCellExperiment(x, path, globals, optionsopt)

Source:

SingleCellExperiment.js, line 111

Parameters:

Name	Type	Attributes	Default	Description
`x`	external:SingleCellExperiment			The single-cell experiment.
`path`	string			Path to the directory in which to save `x`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options.

Returns:

x is stored at path.

(async) saveSummarizedExperiment(x, path, globals, optionsopt)

Source:

SummarizedExperiment.js, line 87

Parameters:

Name	Type	Attributes	Default	Description
`x`	external:SummarizedExperiment			The summarized experiment.
`path`	string			Path to the directory in which to save `x`.
`globals`	object			Object satisfying the GlobalsInterface.
`options`	object	<optional>	`{}`	Further options.

Returns:

x is stored at path.