SummarizedExperiment - Documentation

Constructor

new SummarizedExperiment(assays, optionsopt)

Source:

SummarizedExperiment.js, line 31

Parameters:

Name Type Attributes Default Description

assays

Object | Map

Object or Map where keys are the assay names and values are multi-dimensional arrays of experimental data. All arrays should have the same number of rows and columns.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`assayOrder`	Array	<optional> <nullable>	`null`	Array of strings specifying the ordering of the assays. If non-`null`, this should have the same values as the keys of `assays`. If `null`, an arbitrary ordering is obtained from `assays`.
`rowData`	DataFrame	<optional> <nullable>	`null`	Data frame of row annotations. If non-`null`, this should have a number of rows equal to the number of rows in each entry of `assays`. If `null`, an empty DataFrame is automatically created.
`columnData`	DataFrame	<optional> <nullable>	`null`	Data frame of column annotations. If non-`null`, this should have a number of columns equal to the number of columns in each entry of `assays`. If `null`, an empty DataFrame is automatically created.
`rowNames`	Array	<optional> <nullable>	`null`	Array of strings of length equal to the number of rows in the `assays`, containing row names. Alternatively `null`, if no row names are present.
`columnNames`	Array	<optional> <nullable>	`null`	Array of strings of length equal to the number of columns in the `assays`, containing column names. Alternatively `null`, if no column names are present.
`metadata`	Object \| Map	<optional>	`{}`	Object or Map containing arbitrary metadata as key-value pairs.

Extends

Annotated

Classes

SummarizedExperiment

Methods

$removeAssay(i) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 221

Parameters:

Name	Type	Description
`i`	string \| number	Identity of the assay to add, either by name or index.

Returns:

A reference to this SummarizedExperiment after removing the specified assay.

Type: SummarizedExperiment

$setAssay(i, value) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 258

Parameters:

Name Type Description

Name	Type	Description
`i`	string \| number	Identity of the assay to add, either by name or index. If `i` is a number, the assay at the specified index is replaced. `i` should be non-negative and less than the number of assays. If `i` is a string, any assay with the same name is replaced. If no such assay exists, a new assay is appended to the list of assays.
`value`	*	Multi-dimensional array-like object to set/add as the assay.

i

string | number

Identity of the assay to add, either by name or index.

If i is a number, the assay at the specified index is replaced. i should be non-negative and less than the number of assays.
If i is a string, any assay with the same name is replaced. If no such assay exists, a new assay is appended to the list of assays.

value

Multi-dimensional array-like object to set/add as the assay.

Returns:

A reference to this SummarizedExperiment with modified assays.

Type: SummarizedExperiment

$setAssayNames(names) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 287

Parameters:

Name	Type	Description
`names`	Array	Array of strings containing the assay names. This should be of the same length as the number of assays and contain unique values.

Returns:

A reference to this SummarizedExperiment with modified assay names.

Type: SummarizedExperiment

$setColumnData(value) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 382

Parameters:

Name	Type	Description
`value`	DataFrame	Data frame containing the column annotations. This should have one row for each columns of this SummarizedExperiment.

Returns:

A reference to this SummarizedExperiment with modified column data.

Type: SummarizedExperiment

$setColumnNames(names, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 446

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings of length equal to the number of columns in this SummarizedExperiment, containing column names. Alternatively null, to remove all column names.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with modified column names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

$setMetadata(value) → {Annotated}

Source:

Annotated.js, line 55

Overrides:

Annotated#$setMetadata

Parameters:

Name	Type	Description
`value`	Object	Object containing the metadata.

Returns:

A reference to this Annotated object.

Type: Annotated

$setRowData(value) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 349

Parameters:

Name	Type	Description
`value`	DataFrame	Data frame containing the row annotations. This should have one row for each row of this SummarizedExperiment.

Returns:

A reference to this SummarizedExperiment with modified row data.

Type: SummarizedExperiment

$setRowNames(names) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 412

Parameters:

Name	Type	Description
`names`	Array	Array of strings of length equal to the number of rows in this SummarizedExperiment, containing row names. Alternatively `null`, to remove all row names.

Returns:

A reference to this SummarizedExperiment with modified row names.

Type: SummarizedExperiment

$sliceAssays(i) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 316

Parameters:

Name	Type	Description
`i`	Array	Array of strings or indices specifying the assays to retain in the slice. This should refer to unique assay names.

Returns:

A reference to this SummarizedExperiment with sliced assays.

Type: SummarizedExperiment

assay(i) → {*}

Source:

SummarizedExperiment.js, line 142

Parameters:

Name	Type	Description
`i`	string \| number	Assay to retrieve, either by name or index.

Returns:

The contents of assay i as an multi-dimensional array-like object.

Type: *

assayNames() → {Array}

Source:

SummarizedExperiment.js, line 127

Returns:

Array of assay names.

Type: Array

columnData() → {DataFrame}

Source:

SummarizedExperiment.js, line 176

Returns:

Data frame of column data, with one row per column in this SummarizedExperiment.

Type: DataFrame

columnNames() → (nullable) {Array}

Source:

SummarizedExperiment.js, line 190

Returns:

Array of strings containing column names, or null if no column names are available.

Type: Array

metadata() → {Map}

Source:

Annotated.js, line 28

Overrides:

Annotated#metadata

Returns:

Map containing arbitrary metadata.

Type: Map

numberOfAssays() → {number}

Source:

SummarizedExperiment.js, line 134

Returns:

Number of assays.

Type: number

numberOfColumns() → {number}

Source:

SummarizedExperiment.js, line 183

Returns:

Number of columns in this SummarizedExperiment.

Type: number

numberOfRows() → {number}

Source:

SummarizedExperiment.js, line 162

Returns:

Number of rows in this SummarizedExperiment.

Type: number

removeAssay(i, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 207

Parameters:

Name Type Attributes Default Description

i

string | number

Identity of the assay to add, either by name or index.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment after removing the specified assay. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

rowData() → {DataFrame}

Source:

SummarizedExperiment.js, line 155

Returns:

Data frame of row data, with one row per row in this SummarizedExperiment.

Type: DataFrame

rowNames() → (nullable) {Array}

Source:

SummarizedExperiment.js, line 169

Returns:

Array of strings containing row names, or null if no row names are available.

Type: Array

setAssay(i, value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 239

Parameters:

Name Type Attributes Default Description

i

string | number

Identity of the assay to add, either by name or index.

If i is a number, the assay at the specified index is replaced. i should be non-negative and less than the number of assays.
If i is a string, any assay with the same name is replaced. If no such assay exists, a new assay is appended to the list of assays.

value

Multi-dimensional array-like object to set/add as the assay.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

A SummarizedExperiment with modified assays. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

setAssayNames(names, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 272

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings containing the assay names. This should be of the same length as the number of assays and contain unique values.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with modified assay names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

setColumnData(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 363

Parameters:

Name Type Attributes Default Description

value

DataFrame

Data frame containing the column annotations. This should have one row for each columns of this SummarizedExperiment.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with modified column data. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

setColumnNames(names, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 426

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings of length equal to the number of columns in this SummarizedExperiment, containing column names. Alternatively null, to remove all column names.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with modified column names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

setMetadata(value, optionsopt) → {Annotated}

Source:

Annotated.js, line 45

Overrides:

Annotated#setMetadata

Parameters:

Name Type Attributes Default Description

value

Object | Map

Object containing the metadata.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this Annotated instance in place. If `false`, a new instance is returned.

Returns:

The Annotated object after replacing the metadata. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: Annotated

setRowData(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 330

Parameters:

Name Type Attributes Default Description

value

DataFrame

Data frame containing the row annotations. This should have one row for each row of this SummarizedExperiment.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with modified row data. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

setRowNames(names, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 396

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings of length equal to the number of rows in this SummarizedExperiment, containing row names. Alternatively null, to remove all row names.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with modified row names. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment

sliceAssays(i, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 301

Parameters:

Name Type Attributes Default Description

i

Array

Array of strings or indices specifying the assays to retain in the slice. This should refer to unique assay names.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with sliced assays. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SummarizedExperiment