ZippedAlabasterDataset

ZippedAlabasterDataset

Dataset as a ZIP file containing a SummarizedExperiment in the alabaster representation. Specifically, the ZIP file should contain the contents of an alabaster project directory. This project directory may contain multiple objects; the SummarizedExperiment of interest is identified in the constructor.

Constructor

new ZippedAlabasterDataset(prefix, zipfile, optionsopt)

Source:
Parameters:
Name Type Attributes Default Description
prefix string

Name of the SummarizedExperiment object inside the ZIP file. This should be . if the OBJECT file is stored at the root of the ZIP file, otherwise it should be the relative path to the object directory containing the OBJECT file.
zipfile SimpleFile | string | File

Contents of the ZIP file containing the project directory. On browsers, this may be a File object. On Node.js, this may also be a string containing a file path.
options object <optional>
 {}

Optional parameters.

Properties
Name Type Attributes Default Description
existingHandle JSZip <optional>
<nullable>
 null

An existing handle into the ZIP file, generated using the JSZip package. If an existing handle already exists, passing it in here will allow it to be re-used for greater efficiency. If null, a new handle is created for this ZippedAlabasterDataset instance.

Extends

Classes

ZippedAlabasterDataset

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 summary.

Source:
Overrides:

(async) load(optionsopt) → {object}

Source:
Overrides:
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:
Overrides:
Returns:

Object containing all options used for loading.

Type
object

(async) previewPrimaryIds(optionsopt) → {object}

Source:
Overrides:
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.

If the main experiment is unnamed, its modality name is set to an empty string. If the main experiment's name is the same as any alternative experiment name, the former will be reported in the returned object.

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:
Overrides:
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 <optional>
<nullable>

Name of the main/alternative experiment containing gene expression data, as reported in the keys of the modality_assay_names of summary). If i is null or the name does not exist, it is ignored and no RNA data is assumed to be present.
adtExperiment string <optional>
<nullable>

Name of the main/alternative experiment containing ADT data, as reported in the keys of the modality_assay_names of summary). If i is null or the name does not exist, it is ignored and no ADTs are assumed to be present.
crisprExperiment string <optional>
<nullable>

Name of the main/alternative experiment containing CRISPR guide data, as reported in the keys of the modality_assay_names of summary). If i is null or the name does not exist, it is ignored and no CRISPR guides are assumed to be present.
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.

(async) summary(optionsopt) → {object}

Source:
Overrides:
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.

If the main experiment is unnamed, its modality name is set to an empty string. If the main experiment's name is the same as any alternative experiment name, the former will be reported in the returned objects.

Type
object

(static) format() → {string}

Source:
Returns:

String specifying the format for this dataset.

Type
string

(static) unserialize(files, options) → {ZippedAlabasterDataset}

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
ZippedAlabasterDataset