SummarizedExperimentResult

SummarizedExperimentResult

Pre-computed analysis results stored as a SummarizedExperiment object (or one of its subclasses) inside an RDS file.

Constructor

new SummarizedExperimentResult(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

SummarizedExperimentResult

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 {@linkcodeSummarizedExperimentResult#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 results for re-use in subsequent calls to this method or summary. 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.
  • reduced_dimensions: an object containing the dimensionality reduction results. Each value is an array of arrays, where each inner array contains the coordinates for one dimension.

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

options() → {object}

Source:
Returns:

Object containing all options used for loading.

Type
object

setOptions(options)

Source:
Parameters:
Name Type Description
options object

Optional parameters that affect load (but not summary).

Properties
Name Type Attributes Description
primaryAssay object | string | number <optional>

Assay containing the relevant data for each modality.

  • If a string, this is used as the name of the assay across all modalities.
  • If a number, this is used as the index of the assay across all modalities.
  • If any object, the key should be the name of a modality and the value may be either a string or number specifying the assay to use for that modality. Modalities absent from this object will not be loaded.
isPrimaryNormalized object | boolean <optional>

Whether or not the assay for a particular modality has already been normalized.

  • If a boolean, this is used to indicate normalization status of assays across all modalities. If false, that modality's assay is assumed to contain count data and is subjected to library size normalization.
  • If any object, the key should be the name of a modality and the value should be a boolean indicating whether that modality's assay has been normalized. Modalities absent from this object are assumed to have been normalized.
reducedDimensionNames Array <optional>
<nullable>

Array of names of the reduced dimensions to load. If null, all reduced dimensions found in the file are loaded.

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 results for re-use in subsequent calls to this method or load. 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.
  • reduced_dimension_names: an Array of strings containing names of dimensionality reduction results.

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