get_decomposed_data: Decomposes SpatialRNA data into individual cells

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

Decomposes SpatialRNA data into individual cells

Description

Warning: in the current RCTD version, this function is deprecated, and is no longer supported. For differential expression tasks, we instead recommend the RCTDE method.

Usage

get_decomposed_data(
  results_df,
  gene_list,
  puck,
  weights_doublet,
  cell_type_info
)

Arguments

results_df	a dataframe of RCTD results
gene_list	a list of genes to be used for the decomposition
puck	an object of type SpatialRNA
weights_doublet	a dataframe of predicted weights in doublet mode
cell_type_info	cell type information and profiles of each cell, calculated from the scRNA-seq reference (see get_cell_type_info)

Details

Applied to the output of gather_results. Singlet pixels are left unchanged, and doublet_certain conditions are decomposed into single cells.

Value

An object of type SpatialRNA representing the decomposed cells

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