buildReference: Function for building a Symphony reference starting from expression matrix

Description

Function for building a Symphony reference starting from expression matrix

Usage

buildReference(
  exp_ref,
  metadata_ref,
  vars = NULL,
  K = 100,
  verbose = FALSE,
  do_umap = TRUE,
  do_normalize = TRUE,
  vargenes_method = "vst",
  vargenes_groups = NULL,
  topn = 2000,
  tau = 0,
  theta = 2,
  save_uwot_path = NULL,
  d = 20,
  additional_genes = NULL,
  umap_min_dist = 0.1,
  seed = 111
)

Value

Symphony reference object. Integrated embedding is stored in the $Z_corr slot. Other slots include cell-level metadata ($meta_data), variable genes means and standard deviations ($vargenes), loadings from PCA ($loadings), original PCA embedding ($Z_orig), reference compression terms ($cache), betas from Harmony integration ($betas), cosine normalized soft cluster centroids ($centroids), centroids in PC space ($centroids_pc), and optional umap coordinates ($umap$embedding).

Arguments

exp_ref: Reference gene expression (genes by cells)
metadata_ref: Reference cell metadata (cells by attributes)
vars: Reference variables to Harmonize over e.g. c('donor', 'technology')
K: Number of soft cluster centroids in model
verbose: Verbose output
do_umap: Perform UMAP visualization on harmonized reference embedding
do_normalize: Perform log(CP10K+1) normalization
vargenes_method: Variable gene selection method (either 'vst' or 'mvp')
vargenes_groups: Name of metadata column specifying groups for variable gene selection. If not NULL, calculate topn variable genes in each group separately, then pool
topn: Number of variable genes to subset by
tau: Tau parameter for Harmony step
theta: Theta parameter(s) for Harmony step
save_uwot_path: Absolute path to save the uwot model (used if do_umap is TRUE)
d: Number of PC dimensions
additional_genes: Any custom genes (e.g. marker genes) to include in addition to variable genes
umap_min_dist: umap parameter (see uwot documentation for details)
seed: Random seed