ExtendGates: Extend gating to unassigned cells

In davnovak/SingleBench: Framework for benchmarking and optimising dimension-reduction and clustering pipelines in expression data analysis

Description

Uses a k-NN classifier to label cells that are marked as 'unassigned' in an existing manual annotation vector. A majority vote is taken among nearest neighbours to an unassigned cells, excluding other unassigneds. This procedure can be repeated in multiple consecutive iterations.

Usage

ExtendGates(
  exprs,
  annotation,
  unassigned_labels,
  knn_indices,
  k = NULL,
  n_iter = 1,
  verbose = TRUE
)

Arguments

exprs	numeric matrix: a coordinate matrix of biological expression data (columns correspond to markers, rows correspond to cells)
annotation	string or factor vector: vector of labels per each row of exprs
unassigned_labels	string or string vector: names of population labels to handle as 'unassigned' events (not belonging to a manually annotated population)
knn_indices	numeric matrix: the Indices slot of a k-NN object produced by the function ComputekNNMatrix
k	integer: number of nearest neighbours of each point to use for labelling. Default value is the maximum possible value (k of the k-NN matrix)
n_iter	integer: number of labelling iterations. Default value is 1
verbose	logical: whether to display progress messages. Default value is TRUE

See Also

• ComputekNNMatrix: finds k nearest neighbours to each point in high-dimensional expression data

davnovak/SingleBench documentation built on Dec. 19, 2021, 9:10 p.m.