AbstractAlabasterDataset

AbstractAlabasterDataset

Dataset stored as a SummarizedExperiment in the alabaster format. This is intended as a virtual base class; applications should define subclasses that are tied to a specific AlabasterProjectNavigator class. Subclasses should define abbreviate() and serialize() methods, as well as the static format() and unserialize() methods - see the Dataset contract for more details.

Constructor

new AbstractAlabasterDataset(navigator)

Source:
Parameters:
Name Type Description
navigator AlabasterProjectNavigator

A navigator object that describes how to obtain files from the alabaster-formatted object directory.

Classes

AbstractAlabasterDataset

Methods

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:

(async) 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

(async) 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.

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

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 <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:
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) defaults() → {object}

Source:
Returns:

Default options, see setOptions for more details.

Type
object