computeKNNWeights-phylo-method: Compute for each vector the weights to apply to it's K...

In YosefLab/FastProjectR: Functional interpretation of single cell RNA-seq latent manifolds

Compute for each vector the weights to apply to it's K nearest neighbors

Description

Compute for each vector the weights to apply to it's K nearest neighbors

Usage

## S4 method for signature 'phylo'
computeKNNWeights(
  object,
  K = round(sqrt(length(object$tip.label))),
  lcaKNN = FALSE,
  minSize = 20
)

Arguments

object	tree to use for KNN
K	Number of neighbors to consider.
lcaKNN	whether to use LCA based KNN (cluster by minimum size), if false defaults to cophenetic distance (random tie breaking). WARNING: lcaKNN doesn't perform well with broad multifurcations

Value

a list of two items: indices: matrix, cells X neighbors Each row specifies indices of nearest neighbors weights: matrix, cells X neighbors Corresponding weights to nearest neighbors

YosefLab/FastProjectR documentation built on Feb. 15, 2023, 6:21 a.m.