AnchorCorrection: Run all methods for anchor correction

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

Run all methods for anchor correction

Description

Run all methods for anchor correction

Usage

AnchorCorrection(
  ref_mat,
  query_mat,
  rna_mat,
  cite_index,
  num.cc = NULL,
  k.anchor = 20,
  k.filter = 100,
  k.score = 80,
  k.weight = 100,
  verbose = FALSE
)

Arguments

ref_mat	a (cell x feature) protein expression matrix
query_mat	a (cell x feature) 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
num.cc	number of canonical vectors to calculate. Defaults to number of proteins - 1
k.anchor	number of nn used to find anchors via mutual nearest neighbors
k.filter	number of nn in original feature space to use for filtering
k.score	number of nn to use in shared nearest neighbor scoring
k.weight	number of nn in original query feature space to make correction vectors
verbose	print status at each step

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