SingleCellExperiment - Documentation

Constructor

new SingleCellExperiment(assays, optionsopt)

Source:

SingleCellExperiment.js, line 27

Parameters:

Name Type Attributes Default Description

assays

Object

Object where keys are the assay names and values are multi-dimensional arrays of experimental data.

options

Object

{}

Optional parameters, including those used in the RangedSummarizedExperiment constructor.

Properties

Name	Type	Attributes	Default	Description
`rowRanges`	GRanges \| GroupedGRanges	<optional> <nullable>	`null`	Genomic ranges corresponding to each row, see the RangedSummarizedExperiment constructor.
`reducedDimensions`	Object \| Map	<optional>	`{}`	Object containing named reduced dimensions. Each value should be a 2-dimensional object with number of rows equal to the number of columns of the assays.
`reducedDimensionOrder`	Array	<optional> <nullable>	`null`	Array containing the order of the reduced dimensions. This should have the same values as the keys of `reducedDimensions`, and defaults to those keys if `null`.
`alternativeExperiments`	Object \| Map	<optional>	`{}`	Object containing named alternative experiments. Each value should be a 2-dimensional object with number of columns equal to that of the assays.
`alternativeExperimentOrder`	Array	<optional> <nullable>	`null`	Array containing the order of the alternative experiments. This should have the same values as the keys of `alternativeExperiments`, and defaults to those keys if `null`.
`mainExperimentName`	string	<optional> <nullable>	`null`	Main experiment name, possibly `null` if the main experiment is unnamed.

Extends

RangedSummarizedExperiment

Classes

SingleCellExperiment

Methods

alternativeExperiment(i) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 128

Parameters:

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

Returns:

The specified alternative experiment i.

Type: SummarizedExperiment

alternativeExperimentNames() → {Array}

Source:

SingleCellExperiment.js, line 120

Returns:

Array of strings containing the (ordered) names of the alternative experiments.

Type: Array

alternativeExperiments() → {Map}

Source:

SingleCellExperiment.js, line 141

Returns:

Map where keys are the names and values are the alternative experiments.

Type: Map

assay(i) → {*}

Source:

SummarizedExperiment.js, line 145

Overrides:

RangedSummarizedExperiment#assay

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 130

Overrides:

RangedSummarizedExperiment#assayNames

Returns:

Array of assay names.

Type: Array

assays() → {Map}

Source:

SummarizedExperiment.js, line 158

Overrides:

RangedSummarizedExperiment#assays

Returns:

Map where keys are the assay names and values are the assays.

Type: Map

columnData() → {DataFrame}

Source:

SummarizedExperiment.js, line 186

Overrides:

RangedSummarizedExperiment#columnData

Returns:

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

Type: DataFrame

columnNames() → (nullable) {Array}

Source:

SummarizedExperiment.js, line 200

Overrides:

RangedSummarizedExperiment#columnNames

Returns:

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

Type: Array

mainExperimentName() → (nullable) {string}

Source:

SingleCellExperiment.js, line 148

Returns:

The name of the main experiment, possibly null if this is unnamed.

Type: string

metadata() → {List}

Source:

Annotated.js, line 36

Overrides:

RangedSummarizedExperiment#metadata

Returns:

List of arbitrary metadata.

Type: List

numberOfAssays() → {number}

Source:

SummarizedExperiment.js, line 137

Overrides:

RangedSummarizedExperiment#numberOfAssays

Returns:

Number of assays.

Type: number

numberOfColumns() → {number}

Source:

SummarizedExperiment.js, line 193

Overrides:

RangedSummarizedExperiment#numberOfColumns

Returns:

Number of columns in this SummarizedExperiment.

Type: number

numberOfRows() → {number}

Source:

SummarizedExperiment.js, line 172

Overrides:

RangedSummarizedExperiment#numberOfRows

Returns:

Number of rows in this SummarizedExperiment.

Type: number

reducedDimension(i) → {*}

Source:

SingleCellExperiment.js, line 100

Parameters:

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

Returns:

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

Type: *

reducedDimensionNames() → {Array}

Source:

SingleCellExperiment.js, line 92

Returns:

Array of strings containing the (ordered) names of the reduced dimensions.

Type: Array

reducedDimensions() → {Map}

Source:

SingleCellExperiment.js, line 113

Returns:

Map where keys are the names and values are the reduced dimensions.

Type: Map

removeAlternativeExperiment(i, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 312

Parameters:

Name Type Attributes Default Description

i

string | number

Identity of the reduced dimension to remove, either by name or index.

options

Object

{}

Optional parameters.

Properties

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

Returns:

The SingleCellExperiment 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: SingleCellExperiment

removeAssay(i, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 217

Overrides:

RangedSummarizedExperiment#removeAssay

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

removeReducedDimension(i, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 165

Parameters:

Name Type Attributes Default Description

i

string | number

Identity of the reduced dimension to remove, either by name or index.

options

Object

{}

Optional parameters.

Properties

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

Returns:

The SingleCellExperiment 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: SingleCellExperiment

rowData() → {DataFrame}

Source:

SummarizedExperiment.js, line 165

Overrides:

RangedSummarizedExperiment#rowData

Returns:

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

Type: DataFrame

rowNames() → (nullable) {Array}

Source:

SummarizedExperiment.js, line 179

Overrides:

RangedSummarizedExperiment#rowNames

Returns:

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

Type: Array

rowRanges() → {GRanges}

Source:

RangedSummarizedExperiment.js, line 72

Overrides:

RangedSummarizedExperiment#rowRanges

Returns:

Genomic ranges corresponding to each row.

Type: GRanges

setAlternativeExperiment(i, value, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 340

Parameters:

Name Type Attributes Default Description

i

string | number

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

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

value

SummarizedExperiment

A SummarizedExperiment to set/add as the alternative experiment.

options

Object

{}

Optional parameters.

Properties

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

Returns:

The SingleCellExperiment with modified alternative experiments. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SingleCellExperiment

setAlternativeExperimentNames(names, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 363

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings containing the alternative experiment names. This should be of the same length as the number of alternative experiments and contain unique values.

options

Object

{}

Optional parameters.

Properties

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

Returns:

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

Type: SingleCellExperiment

setAlternativeExperiments(value, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 392

Parameters:

Name Type Attributes Default Description

value

Object | Map

Object containing zero, one or more SummarizedExperiment objects in the values. Each value should have the same number of columns as this SingleCellExperiment. Keys are alternative experiment names, each of which should be present in order.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SingleCellExperiment instance in place. If `false`, a new instance is returned.
`newOrder`	Array \| boolean	<optional>	`false`	Whether to replace the order of alternative experiments with the order of keys in `value`. If `false`, the existing order in `alternativeExperimentNames` is used. If an array is provided, this is used as the order. If `null`, this has the same effect as `true`.

Returns:

A SingleCellExperiment with the new alternative experiments. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SingleCellExperiment

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

Source:

SummarizedExperiment.js, line 245

Overrides:

RangedSummarizedExperiment#setAssay

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 315

Overrides:

RangedSummarizedExperiment#setAssayNames

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

setAssays(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 269

Overrides:

RangedSummarizedExperiment#setAssays

Parameters:

Name Type Attributes Default Description

value

Object | Map

Object containing zero, one or more multi-dimensional array-like objects in the values. All arrays should have the same number of rows and columns. Keys are assay names, each of which should be present in order.

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.
`newOrder`	Array \| boolean	<optional>	`false`	Whether to replace the order of assays with the order of keys in `value`. If `false`, the existing order in `assayNames` is used. If an array is provided, this is used as the order. If `null`, this has the same effect as `true`.

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

setColumnData(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 391

Overrides:

RangedSummarizedExperiment#setColumnData

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 443

Overrides:

RangedSummarizedExperiment#setColumnNames

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

setMainExperimentName(optionsopt) → (nullable) {string|SingleCellExperiment}

Source:

SingleCellExperiment.js, line 454

Parameters:

Name Type Attributes Default Description

options

Object

{}

Optional parameters.

Properties

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

Returns:

name - The name of the main experiment, possibly null if this is unnamed.

Type

string
A SingleCellExperiment with a new main experiment name. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type

SingleCellExperiment

setMetadata(value, optionsopt) → {Annotated}

Source:

Annotated.js, line 53

Overrides:

RangedSummarizedExperiment#setMetadata

Parameters:

Name Type Attributes Default Description

value

Object | Map | Array | List

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

setReducedDimension(i, value, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 193

Parameters:

Name Type Attributes Default Description

i

string | number

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

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

value

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

options

Object

{}

Optional parameters.

Properties

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

Returns:

The SingleCellExperiment with modified reduced dimensions. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SingleCellExperiment

setReducedDimensionNames(names, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 216

Parameters:

Name Type Attributes Default Description

names

Array

Array of strings containing the reduced dimension names. This should be of the same length as the number of reduced dimensions and contain unique values.

options

Object

{}

Optional parameters.

Properties

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

Returns:

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

Type: SingleCellExperiment

setReducedDimensions(value, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 245

Parameters:

Name Type Attributes Default Description

value

Object | Map

Object containing zero, one or more multi-dimensional array-like objects in the values. Each value should be a 2-dimensional object with number of rows equal to the number of columns in this SingleCellExperiment. Keys are reduced dimension names, each of which should be present in order.

options

Object

{}

Optional parameters.

Properties

Name	Type	Attributes	Default	Description
`inPlace`	boolean	<optional>	`false`	Whether to mutate this SingleCellExperiment instance in place. If `false`, a new instance is returned.
`newOrder`	Array \| boolean	<optional>	`false`	Whether to replace the order of reduced dimensions with the order of keys in `value`. If `false`, the existing order in `reducedDimensionNames` is used. If an array is provided, this is used as the order. If `null`, this has the same effect as `true`.

Returns:

A SingleCellExperiment with the new reduced dimensions. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: SingleCellExperiment

setRowData(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 363

Overrides:

RangedSummarizedExperiment#setRowData

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 419

Overrides:

RangedSummarizedExperiment#setRowNames

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

setRowRanges(value, optionsopt) → {RangedSummarizedExperiment}

Source:

RangedSummarizedExperiment.js, line 90

Overrides:

RangedSummarizedExperiment#setRowRanges

Parameters:

Name Type Attributes Default Description

value

GRanges

Genomic ranges corresponding to each row. This should have length equal to the number of rows in this RangedSummarizedExperiment.

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 RangedSummarizedExperiment after modifying its rowRanges. If inPlace = true, this is a reference to the current instance, otherwise a new instance is created and returned.

Type: RangedSummarizedExperiment

sliceAlternativeExperiments(i, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 432

Parameters:

Name Type Attributes Default Description

i

Array

Array of strings or indices specifying the alternative experiments to retain in the slice. This should refer to unique alternative experiment names.

options

Object

{}

Optional parameters.

Properties

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

Returns:

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

Type: SingleCellExperiment

sliceAssays(i, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 339

Overrides:

RangedSummarizedExperiment#sliceAssays

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

sliceReducedDimensions(i, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 285

Parameters:

Name Type Attributes Default Description

i

Array

Array of strings or indices specifying the reduced dimensions to retain in the slice. This should refer to unique reduced dimension names.

options

Object

{}

Optional parameters.

Properties

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

Returns:

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

Type: SingleCellExperiment