mapQuery: Function for mapping query cells to a Symphony reference

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

Function for mapping query cells to a Symphony reference

Description

Function for mapping query cells to a Symphony reference

Usage

mapQuery(
  exp_query,
  metadata_query,
  ref_obj,
  vars = NULL,
  verbose = TRUE,
  do_normalize = TRUE,
  do_umap = TRUE,
  sigma = 0.1
)

Arguments

exp_query	Query gene expression (genes by cells)
metadata_query	Query metadata (cells by attributes)
ref_obj	Reference object as returned by Symphony buildReference()
vars	Query batch variable(s) to integrate over (column names in metadata)
verbose	Verbose output
do_normalize	Perform log(CP10K+1) normalization on query expression
do_umap	Perform umap projection into reference UMAP (if reference includes a uwot model)
sigma	Fuzziness parameter for soft clustering (sigma = 1 is hard clustering)

Value

Symphony query object. Mapping embedding is in the $Z slot. Other slots include query expression matrix ($exp), query cell-level metadata ($meta_data), query cell embedding in pre-Harmonized reference PCs ($Zq_pca), query cell soft cluster assignments ($R), and query cells in reference UMAP coordinates ($umap).

symphony documentation built on Jan. 17, 2023, 1:13 a.m.