buildReference: Function for building a Symphony reference starting from...

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

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
)

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

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).

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