SummarizedExperimentDataset

SummarizedExperimentDataset

Dataset stored as a SummarizedExperiment object (or one of its subclasses) inside an RDS file.

Constructor

new SummarizedExperimentDataset(rdsFile)

Source:
Parameters:
Name Type Description
rdsFile SimpleFile | string | Uint8Array | File

Contents of a RDS file. On browsers, this may be a File object. On Node.js, this may also be a string containing a file path.

Classes

SummarizedExperimentDataset

Methods

abbreviate() → {object}

Source:
Returns:

Object containing the abbreviated details of this dataset.

Type
object

clear()

Description:

  • Destroy caches if present, releasing the associated memory. This may be called at any time but only has an effect if cache = true in load or {@linkcodeSummarizedExperimentDataset#summary summary}.

Source:

load(optionsopt) → {object}

Source:
Parameters:
Name Type Attributes Default Description
options object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
cache boolean <optional>
 false

Whether to cache the intermediate results for re-use in subsequent calls to any methods with a cache option. If true, users should consider calling clear to release the memory once this dataset instance is no longer needed.
Returns:

Object containing the per-feature and per-cell annotations. This has the following properties:

  • features: an object where each key is a modality name and each value is a DataFrame of per-feature annotations for that modality.
  • cells: a DataFrame containing per-cell annotations.
  • matrix: a MultiMatrix containing one ScranMatrix per modality.
  • primary_ids: an object where each key is a modality name and each value is an array (usually of strings) containing the primary feature identifiers for each row in that modality.

Modality names are guaranteed to be one of "RNA", "ADT" or "CRISPR". We assume that the instance already contains an appropriate mapping from the observed feature types to each expected modality, either from the defaults or with setOptions.

Type
object

options() → {object}

Source:
Returns:

Object containing all options used for loading.

Type
object

previewPrimaryIds(optionsopt) → {object}

Source:
Parameters:
Name Type Attributes Default Description
options object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
cache boolean <optional>
 false

Whether to cache the intermediate results for re-use in subsequent calls to any methods with a cache option. If true, users should consider calling clear to release the memory once this dataset instance is no longer needed.
Returns:

An object where each key is a modality name and each value is an array (usually of strings) containing the primary feature identifiers for each row in that modality. The contents are the same as the primary_ids returned by load but the order of values may be different.

Type
object

serialize() → {object}

Source:
Returns:

Object describing this dataset, containing:

  • files: Array of objects representing the files used in this dataset. Each object corresponds to a single file and contains:
    • type: a string denoting the type.
    • file: a SimpleFile object representing the file contents.
  • options: An object containing additional options to saved.
Type
object

setOptions(options)

Source:
Parameters:
Name Type Description
options object

Optional parameters that affect load (but not summary).

Properties
Name Type Attributes Description
rnaCountAssay string | number <optional>

Name or index of the assay containing the RNA count matrix.
adtCountAssay string | number <optional>

Name or index of the assay containing the ADT count matrix.
crisprCountAssay string | number <optional>

Name or index of the assay containing the CRISPR count matrix.
rnaExperiment string | number <optional>
<nullable>

Name or index of the alternative experiment containing gene expression data.

If i is null or invalid (e.g., out of range index, unavailable name), it is ignored and no RNA data is assumed to be present. If i is an empty string, the main experiment is assumed to contain the gene expression data.
adtExperiment string | number <optional>
<nullable>

Name or index of the alternative experiment containing ADT data.

If i is null or invalid (e.g., out of range index, unavailable name), it is ignored and no ADTs are assumed to be present. If i is an empty string, the main experiment is assumed to contain the ADT data.
crisprExperiment string | number <optional>
<nullable>

Name or index of the alternative experiment containing CRISPR guide data.

If i is null or invalid (e.g., out of range index, unavailable name), it is ignored and no CRISPR guides are assumed to be present. If i is an empty string, the main experiment is assumed to contain the guide data.
primaryRnaFeatureIdColumn string | number <optional>
<nullable>

Name or index of the column of the features DataFrame that contains the primary feature identifier for gene expression.

If i is null or invalid (e.g., out of range index, unavailable name), it is ignored and the primary identifier is defined as the existing row names. However, if no row names are present in the SummarizedExperiment, no primary identifier is defined.
primaryAdtFeatureIdColumn string | number <optional>
<nullable>

Name or index of the column of the features DataFrame that contains the primary feature identifier for the ADTs.

If i is null or invalid (e.g., out of range index, unavailable name), it is ignored and the primary identifier is defined as the existing row names. However, if no row names are present in the SummarizedExperiment, no primary identifier is defined.
primaryCrisprFeatureIdColumn string | number <optional>
<nullable>

Name or index of the column of the features DataFrame that contains the primary feature identifier for the CRISPR guides.

If i is null or invalid (e.g., out of range index, unavailable name), it is ignored and the existing row names (if they exist) are used as the primary identifier. However, if no row names are present in the SummarizedExperiment, no primary identifier is defined.

summary(optionsopt) → {object}

Source:
Parameters:
Name Type Attributes Default Description
options object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
cache boolean <optional>
 false

Whether to cache the intermediate results for re-use in subsequent calls to any methods with a cache option. If true, users should consider calling clear to release the memory once this dataset instance is no longer needed.
Returns:

Object containing the per-feature and per-cell annotations. This has the following properties:

  • modality_features: an object where each key is a modality name and each value is a DataFrame of per-feature annotations for that modality.
  • cells: a DataFrame of per-cell annotations.
  • modality_assay_names: an object where each key is a modality name and each value is an Array containing the names of available assays for that modality. Unnamed assays are represented as null names.
Type
object

(static) defaults() → {object}

Source:
Returns:

Default options, see setOptions for more details.

Type
object

(static) format() → {string}

Source:
Returns:

Format of this dataset class.

Type
string

(async, static) unserialize(files, options) → {SummarizedExperimentDataset}

Source:
Parameters:
Name Type Description
files Array

Array of objects like that produced by serialize.
options object

Object containing additional options to be passed to the constructor.
Returns:

A new instance of this class.

Type
SummarizedExperimentDataset