KNN imputation (for replication)

The function imputes missing data using the k-nearest neighbours (KNN) approach using Euclidean distance as a similarity measure between the cells. This function was provided as part of the SCoPE2 publication (Specht et al. 2021).

imputeKnnSCoPE2(object, i, name = "KNNimputedAssay", k = 3)

Source

The implementation of the imputation was retrieved from https://github.com/SlavovLab/SCoPE2

Arguments

object

A QFeatures object

i

A numeric() or character() vector indicating from which assays the rowData should be taken.

name

A character(1) naming the new assay name. Default is KNNimputedAssay.

k

An integer(1) giving the number of neighbours to use.

Value

An object of class QFeatures containing an extra assay with imputed values.

References

Specht, Harrison, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko, Antonius Koller, and Nikolai Slavov. 2021. “Single-Cell Proteomic and Transcriptomic Analysis of Macrophage Heterogeneity Using SCoPE2.” Genome Biology 22 (1): 50.