report_cell_metrics: Reports BEARscc metrics for cells.

Description Usage Arguments Value Author(s) Examples

Description

To quantitatively evaluate the results, three metrics are calculated from the noise consensus matrix: 'stability' is the average frequency with which cells within a cluster associate with each other across simulated replicates; 'promiscuity' measures the association frequency between cells within a cluster and those outside of it; and 'score' is the difference between 'stability' and 'promiscuity'. Importantly, 'score' reflects the overall "robustness" of a cluster and its constitutive samples to technical variance. These metrics may be calculated on cell or cluster-wise basis; here, they are calculated cell-wise.

Usage

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report_cell_metrics(cluster_labels, consensus_matrix)

Arguments

cluster_labels

Cluster labels for each cell across various cluster numbers and the original clustering.

consensus_matrix

A noise consensus output by compute_consensus()

Value

A melted data.frame of BEARscc metrics for each cell:

[,1] "Cluster.identity" The number of the cluster within the respective clustering
[,2] "Cell" The identifier of the sample in question.
[,3] "Cluster.size" Number of samples in the cluster.
[,4] "Metric" Whether the metric is the BEARscc Score, Promiscuity, or Stability.
[,5] "Value" Value of the relevant BEARscc metric for the cell in a given clustering.
[,6] "Clustering" The clustering pertinant to the cell-wise metrics described.

Author(s)

David T. Severson <david_severson@hms.harvard.edu>

Maintainer: Benjamin Schuster-Boeckler <benjamin.schuster-boeckler@ludwig.ox.ac.uk>

Examples

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BEARscc documentation built on Nov. 8, 2020, 7:56 p.m.