NeighborIndexState

This step assembles the neighbor search indices from the PCs (see PcaState) in preparation for nearest neighbor searches in downstream steps. It wraps the buildNeighborSearchIndex function from scran.js.

Methods not documented here are not part of the stable API and should not be used by applications.

Classes

NeighborIndexState

Methods

compute(parameters)

Description:

This method should not be called directly by users, but is instead invoked by runAnalysis.

Source:

steps/neighbor_index.js, line 89

Parameters:

Name Type Description

parameters

object

Parameter object, equivalent to the neighbor_index property of the parameters of runAnalysis.

Properties

Name	Type	Attributes	Description
`approximate`	boolean	<optional>	Whether to create an approximate search index. If `false`, an exact index is used.

Returns:

The object is updated with the new results.

fetchIndex() → {BuildNeighborSearchIndexResults}

Source:

steps/neighbor_index.js, line 43

Returns:

Index for a nearest-neighbor search, available after running compute.

Type: BuildNeighborSearchIndexResults

fetchParameters() → {object}

Source:

steps/neighbor_index.js, line 53

Returns:

Object containing the parameters.

Type: object

(static) defaults() → {object}

Source:

steps/neighbor_index.js, line 65

Returns:

Object containing default parameters, see the parameters argument in compute for details.

Type: object