calcknncorrWithinQuery: Calculates the k-NN correlation within the query cells only,...

In symphony: Efficient and Precise Single-Cell Reference Atlas Mapping

Calculates the k-NN correlation within the query cells only, which measures how well the sorted ordering of k nearest query neighbors in a query de novo PCA embedding correlate with the ordering for the cells in the reference mapping embedding.

Description

Calculates the k-NN correlation within the query cells only, which measures how well the sorted ordering of k nearest query neighbors in a query de novo PCA embedding correlate with the ordering for the cells in the reference mapping embedding.

Usage

calcknncorrWithinQuery(
  query,
  var = NULL,
  k = 100,
  topn = 2000,
  d = 20,
  distance = "euclidean"
)

Arguments

query	Query object (returned from mapQuery)
var	Query metadata batch variable (PCA is calculated within each batch separately); if NULL, do not split by batch
k	Number of neighbors to use for kNN-correlation calculation
topn	number of variable genes to calculate within each query batch for query PCA
d	number of dimensions for query PCA within each query batch
distance	either 'euclidean' or 'cosine'

Value

Vector of within-query k-NN correlations for query cells

symphony documentation built on Nov. 5, 2025, 7:41 p.m.