CrisprQualityControlState

CrisprQualityControlState

This step applies quality control on the CRISPR guide count matrix. Specifically, it computes the QC metrics and filtering thresholds, wrapping the perCellCrisprQcMetrics and suggestCrisprQcFilters functions from scran.js. Note that the actual filtering is done by CellFilteringState.

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

Classes

CrisprQualityControlState

Methods

compute(parameters)

Description:

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

Source:
Parameters:
Name Type Description
parameters object

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

Properties
Name Type Attributes Description
filter_strategy string <optional>

Strategy for defining a filter threshold for the QC metrics. This can be "automatic" or "manual".
nmads number <optional>

Number of MADs to use for automatically selecting the filter threshold on the maximum count. Only used when filter_strategy = "automatic".
max_threshold number <optional>

Manual threshold on the maximum count for each cell. Cells are only retained if their maximums are greater than or equal to this threshold. Only used when filter_strategy = "manual".
Returns:

The object is updated with the new results.

fetchFilters() → {external:SuggestCrisprQcFiltersResults}

Source:
Returns:

Result of filtering on the CRISPR-derived QC metrics. This is available after running compute.

Type
external:SuggestCrisprQcFiltersResults

fetchKeep() → {Uint8WasmArray}

Source:
Returns:

Buffer containing a vector of length equal to the number of cells, where each element is truthy if the corresponding cell is to be retained after filtering. This is available after running compute.

Type
Uint8WasmArray

fetchMetrics() → {external:PerCellCrisprQcMetricsResults}

Source:
Returns:

CRISPR-derived QC metrics, available after running compute.

Type
external:PerCellCrisprQcMetricsResults

fetchParameters() → {object}

Source:
Returns:

Object containing the parameters.

Type
object

(static) defaults() → {object}

Source:
Returns:

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

Type
object