SingleCellExperiment - Documentation

Constructor

new SingleCellExperiment(assays, optionsopt)

Source:

SingleCellExperiment.js, line 24

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`.

Extends

RangedSummarizedExperiment

Classes

SingleCellExperiment

Methods

$removeAlternativeExperiment(i) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 275

Parameters:

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

Returns:

A reference to this SingleCellExperiment after removing the specified assay.

Type: SingleCellExperiment

$removeAssay(i) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 221

Overrides:

RangedSummarizedExperiment#$removeAssay

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

$removeReducedDimension(i) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 153

Parameters:

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

Returns:

A reference to this SingleCellExperiment after removing the specified assay.

Type: SingleCellExperiment

$setAlternativeExperiment(i, value) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 312

Parameters:

Name Type Description

Name	Type	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`	*	Multi-dimensional array-like object to set/add as the alternative experiment.

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

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

Returns:

A reference to this SingleCellExperiment with modified alternative experiments.

Type: SingleCellExperiment

$setAlternativeExperimentNames(names) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 341

Parameters:

Name	Type	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.

Returns:

A reference to this SummarizedExperiment with modified alternative experiment names.

Type: SummarizedExperiment

$setAssay(i, value) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 258

Overrides:

RangedSummarizedExperiment#$setAssay

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

Overrides:

RangedSummarizedExperiment#$setAssayNames

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

Overrides:

RangedSummarizedExperiment#$setColumnData

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

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

$setMetadata(value) → {Annotated}

Source:

Annotated.js, line 55

Overrides:

RangedSummarizedExperiment#$setMetadata

Parameters:

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

Returns:

A reference to this Annotated object.

Type: Annotated

$setReducedDimension(i, value) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 190

Parameters:

Name Type Description

Name	Type	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.

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.

Returns:

A reference to this SingleCellExperiment with modified reduced dimensions.

Type: SingleCellExperiment

$setReducedDimensionNames(names) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 219

Parameters:

Name	Type	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.

Returns:

A reference to this SummarizedExperiment with modified reduced dimension names.

Type: SummarizedExperiment

$setRowData(value) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 349

Overrides:

RangedSummarizedExperiment#$setRowData

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

Overrides:

RangedSummarizedExperiment#$setRowNames

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

$setRowRanges(value) → {RangedSummarizedExperiment}

Source:

RangedSummarizedExperiment.js, line 99

Overrides:

RangedSummarizedExperiment#$setRowRanges

Parameters:

Name	Type	Description
`value`	GRanges	Genomic ranges corresponding to each row. This should have length equal to the number of rows in this RangedSummarizedExperiment.

Returns:

A reference to this RangedSummarizedExperiment after modifying its rowRanges.

Type: RangedSummarizedExperiment

$sliceAlternativeExperiments(i) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 370

Parameters:

Name	Type	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.

Returns:

A reference to this SummarizedExperiment with sliced alternative experiments.

Type: SummarizedExperiment

$sliceAssays(i) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 316

Overrides:

RangedSummarizedExperiment#$sliceAssays

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

$sliceReducedDimensions(i) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 248

Parameters:

Name	Type	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.

Returns:

A reference to this SummarizedExperiment with sliced reduced dimensions.

Type: SummarizedExperiment

alternativeExperiment(i) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 116

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 108

Returns:

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

Type: Array

assay(i) → {*}

Source:

SummarizedExperiment.js, line 142

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 127

Overrides:

RangedSummarizedExperiment#assayNames

Returns:

Array of assay names.

Type: Array

columnData() → {DataFrame}

Source:

SummarizedExperiment.js, line 176

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 190

Overrides:

RangedSummarizedExperiment#columnNames

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:

RangedSummarizedExperiment#metadata

Returns:

Map containing arbitrary metadata.

Type: Map

numberOfAssays() → {number}

Source:

SummarizedExperiment.js, line 134

Overrides:

RangedSummarizedExperiment#numberOfAssays

Returns:

Number of assays.

Type: number

numberOfColumns() → {number}

Source:

SummarizedExperiment.js, line 183

Overrides:

RangedSummarizedExperiment#numberOfColumns

Returns:

Number of columns in this SummarizedExperiment.

Type: number

numberOfRows() → {number}

Source:

SummarizedExperiment.js, line 162

Overrides:

RangedSummarizedExperiment#numberOfRows

Returns:

Number of rows in this SummarizedExperiment.

Type: number

reducedDimension(i) → {*}

Source:

SingleCellExperiment.js, line 95

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 87

Returns:

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

Type: Array

removeAlternativeExperiment(i, optionsopt) → {SingleCellExperiment}

Source:

SingleCellExperiment.js, line 261

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 207

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 139

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 155

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 169

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 69

Overrides:

RangedSummarizedExperiment#rowRanges

Returns:

Genomic ranges corresponding to each row.

Type: GRanges

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

Source:

SingleCellExperiment.js, line 293

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

Multi-dimensional array-like object 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) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 326

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 SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment 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: SummarizedExperiment

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

Source:

SummarizedExperiment.js, line 239

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 272

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

setColumnData(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 363

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 426

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

setMetadata(value, optionsopt) → {Annotated}

Source:

Annotated.js, line 45

Overrides:

RangedSummarizedExperiment#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

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

Source:

SingleCellExperiment.js, line 171

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) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 204

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 SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment 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: SummarizedExperiment

setRowData(value, optionsopt) → {SummarizedExperiment}

Source:

SummarizedExperiment.js, line 330

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 396

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 87

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) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 355

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 SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

The SummarizedExperiment with sliced alternative experiments. 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

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) → {SummarizedExperiment}

Source:

SingleCellExperiment.js, line 233

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 SummarizedExperiment instance in place. If `false`, a new instance is returned.

Returns:

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

Type: SummarizedExperiment