CrisprNormalizationState

This step performs normalization and log-transformation on the QC-filtered CRISPR count matrix from the CellFilteringState. It wraps the logNormCounts functions from scran.js.

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

Classes

CrisprNormalizationState

Methods

compute(parameters)

Description:

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

Source:

steps/crispr_normalization.js, line 107

Parameters:

Name	Type	Description
`parameters`	object	Parameter object, equivalent to the `crispr_normalization` property of the `parameters` of `runAnalysis`.

Returns:

The object is updated with new results.

fetchNormalizedMatrix() → {external:ScranMatrix}

Source:

steps/crispr_normalization.js, line 58

Returns:

A ScranMatrix object containing the normalized CRISPR abundances, available after running compute.

Type: external:ScranMatrix

fetchParameters() → {object}

Source:

steps/crispr_normalization.js, line 82

Returns:

Object containing the parameters.

Type: object

fetchSizeFactors() → {Float64WasmArray}

Source:

steps/crispr_normalization.js, line 70

Returns:

Array of length equal to the number of cells, containing the CRISPR-derived size factor for each cell. This is available after running compute.

Type: Float64WasmArray