AdtQualityControlState

AdtQualityControlState

This step applies quality control on the ADT count matrix. Specifically, it computes the QC metrics and filtering thresholds, wrapping the perCellAdtQcMetrics and suggestAdtQcFilters 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

AdtQualityControlState

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 adt_quality_control property of the parameters of runAnalysis.

Properties
Name Type Attributes Description
guess_ids boolean <optional>

Automatically choose feature-based parameters based on the feature annotations. Specifically, tag_id_column is set to the column with the most matches to igg_prefix.
tag_id_column string | number <optional>
<nullable>

Name or index of the column of the feature annotations that contains the tag identifiers. If null, the row names are used. Ignored if guess_ids = true.
igg_prefix string <optional>
<nullable>

Prefix of the identifiers for isotype controls. If null, no prefix-based identification is performed.
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 for each metric. Only used when filter_strategy = "automatic".
min_detected_drop number <optional>

Minimum proportional drop in the number of detected features before a cell is to be considered low-quality. Only used when filter_strategy = "automatic".
detected_threshold number <optional>

Manual threshold on the detected number of features for each cell. Cells are only retained if the detected number is equal to or greater than this threshold. Only used when filter_strategy = "manual".
igg_threshold number <optional>

Manual threshold on the isotype control totals for each cell. Cells are only retained if their totals are less than or equal to this threshold. Only used when filter_strategy = "manual".
Returns:

The object is updated with the new results.

fetchFilters() → {external:SuggestAdtQcFiltersResults}

Source:
Returns:

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

Type
external:SuggestAdtQcFiltersResults

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:PerCellAdtQcMetricsResults}

Source:
Returns:

ADT-derived QC metrics, available after running compute.

Type
external:PerCellAdtQcMetricsResults

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