FindNNrna: Find nearest neighbors

In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

Find nearest neighbors

Description

Find nearest neighbors

Usage

FindNNrna(
  ref_emb,
  query_emb,
  rna_mat,
  cite_index = 1,
  k = 300,
  eps = 0,
  verbose = FALSE
)

Arguments

ref_emb	a (cell x feature) embedding of a protein expression matrix
query_emb	a (cell x feature) embedding of protein expression matrix to be corrected
rna_mat	a (cell x feature) embedding of the mRNA expression matrix from CITE-seq
cite_index	which matrix (1 or 2) is the CITE-seq protein expression matrix
k	number of nearest neighbor to find between the matrices
eps	error bound on nearest neighbor search (see eps parameter for nn2)
verbose	...

Value

list of nearest neighbor lists: nnab = for each cell in a, its knn in b nnba = for each cell in b, its knn in a nnbb = knn within b, nnaa = knn within a

CamaraLab/STvEA documentation built on April 2, 2024, 6:07 a.m.