SummarizedExperiment

SummarizedExperiment

An interface to the wobbegong representation of a SummarizedExperiment instance.

Constructor

new SummarizedExperiment(summary, path, fetch_json, fetch_range)

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Parameters:
Name Type Description
summary object

A summary of the SummarizedExperiment contents, according to the wobbegong specifications.
path string

Path to the SummarizedExperiment directory. This may be a relative or absolute path, depending on how the files are hosted.
fetch_json function

A function that accepts path, a path to a file inside path. It should retrieve the contents of path and load them as a JSON object. It may also return a promise that resolves to such an object.
fetch_range function

A function that accepts file (a path to a file inside path), start and end. It should retrieve bytes from path in the interval [start, end) and return a Uint8Array containing those bytes. It may also return a promise that resolves to such a Uint8Array.

Classes

SummarizedExperiment

Methods

(async) alternativeExperiment(i) → (nullable) {SummarizedExperiment}

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Parameters:
Name Type Description
i number | string

Index or name of the alternative experiment to retrieve.
Returns:

A SummarizedExperiment instance representing the alternative experiment i, or null if isSingleCellExperiment is false.

Type
SummarizedExperiment

alternativeExperimentNames() → (nullable) {Array}

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Returns:

Names of the alternative experiments. Alternatively null if isSingleCellExperiment is false.

Type
Array

(async) assay(i) → {Matrix}

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Parameters:
Name Type Description
i number | string

Index or name of the assay to retrieve.
Returns:

A Matrix instance representing the assay matrix i.

Type
Matrix

assayNames() → {Array}

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Returns:

Names of the assays.

Type
Array

(async) columnData() → (nullable) {DataFrame}

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Returns:

A DataFrame instance representing the column data, or null if hasColumnData is false.

Type
DataFrame

hasColumnData() → {boolean}

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Returns:

Whether column data is available.

Type
boolean

hasRowData() → {boolean}

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Returns:

Whether row data is available.

Type
boolean

isSingleCellExperiment() → {boolean}

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Returns:

Whether the underlying object is a SingleCellExperiment.

Type
boolean

numberOfColumns() → {number}

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Returns:

Number of columns.

Type
number

numberOfRows() → {number}

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Returns:

Number of rows.

Type
number

(async) reducedDimension(i) → (nullable) {ReducedDimensionResult}

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Parameters:
Name Type Description
i number | string

Index or name of the reduced dimension result to retrieve.
Returns:

A ReducedDimensionResult instance representing the reduced dimension result i, or null if isSingleCellExperiment is false.

Type
ReducedDimensionResult

reducedDimensionNames() → (nullable) {Array}

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Returns:

Names of the reduced dimensions. Alternatively null if isSingleCellExperiment is false.

Type
Array

(async) rowData() → (nullable) {DataFrame}

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Returns:

A DataFrame instance representing the row data, or null if hasRowData is false.

Type
DataFrame