RnaNormalizationState

This step performs normalization and log-transformation on the QC-filtered matrix from the QualityControlState. It wraps the logNormCounts function from scran.js.

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

Classes

RnaNormalizationState

Methods

compute(parameters)

Description:

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

Source:

steps/rna_normalization.js, line 106

Parameters:

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

Returns:

The object is updated with new results.

fetchNormalizedMatrix() → {external:ScranMatrix}

Source:

steps/rna_normalization.js, line 57

Returns:

A ScranMatrix object containing normalized expression values, available after running compute.

Type: external:ScranMatrix

fetchParameters() → {object}

Source:

steps/rna_normalization.js, line 81

Returns:

Object containing the parameters.

Type: object

fetchSizeFactors() → {Float64WasmArray}

Source:

steps/rna_normalization.js, line 69

Returns:

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

Type: Float64WasmArray