process_data: Runs RCTD in full mode on 'puck'

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

Runs RCTD in full mode on puck

Description

Renormalizes cell_type_means to have average the same as the puck if proportions is given. Then, computes cell type proportions for each pixel in puck.

Usage

process_data(
  puck,
  gene_list,
  cell_type_info,
  proportions = NULL,
  trust_model = FALSE,
  constrain = T,
  OLS = F
)

Arguments

puck	an object of type SpatialRNA, the target dataset
gene_list	a list of genes to be used for RCTD
cell_type_info	cell type information and profiles of each cell, calculated from the scRNA-seq reference (see get_cell_type_info)
proportions	(optional) If given, a named list (for each cell type) of proportion of the cell type on the bulk dataset (not constrained to sum to 1)
constrain	logical whether to constrain the weights to sum to one on each pixel

Value

Returns test_results, a list of three items: (1) conf_mat a confusion matrix (not relevant) (2) weights a dataframe of predicted weights (3) a named list of predicted cell types

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