process_beads_batch: Runs RCTD in doublet mode on 'puck'

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

Runs RCTD in doublet mode on puck

Description

Then, computes cell type proportions for each pixel in puck. Classifies each pixel as 'singlet' or 'doublet' and searches for the cell types on the pixel

Usage

process_beads_batch(
  cell_type_info,
  gene_list,
  puck,
  class_df = NULL,
  constrain = T,
  MAX_CORES = 8,
  MIN.CHANGE = 0.001,
  CONFIDENCE_THRESHOLD = 10,
  DOUBLET_THRESHOLD = 25
)

Arguments

cell_type_info	cell type information and profiles of each cell, calculated from the scRNA-seq reference (see get_cell_type_info)
gene_list	a list of genes to be used for RCTD
puck	an object of type SpatialRNA, the target dataset
class_df	A dataframe returned by get_class_df to map cell types to classes
constrain	logical whether to constrain the weights to sum to one on each pixel
CONFIDENCE_THRESHOLD	(Default 10) the minimum change in likelihood (compared to other cell types) necessary to determine a cell type identity with confidence
DOUBLET_THRESHOLD	(Default 25) the penalty weight of predicting a doublet instead of a singlet for a pixel
max_cores	number of cores to use (will use parallel processing if more than one).

Value

Returns results, a list of RCTD results for each pixel, which can be organized by feeding into gather_results

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.