create.RCTD: Creates an 'RCTD' object from a scRNA-seq reference...

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

Creates an RCTD object from a scRNA-seq reference Reference object and a SpatialRNA object

Description

Creates an RCTD object from a scRNA-seq reference Reference object and a SpatialRNA object

Usage

create.RCTD(
  spatialRNA,
  reference,
  max_cores = 4,
  test_mode = FALSE,
  gene_cutoff = 0.000125,
  fc_cutoff = 0.5,
  gene_cutoff_reg = 2e-04,
  fc_cutoff_reg = 0.75,
  UMI_min = 100,
  UMI_max = 2e+07,
  counts_MIN = 10,
  UMI_min_sigma = 300,
  class_df = NULL,
  CELL_MIN_INSTANCE = 25,
  cell_type_names = NULL,
  MAX_MULTI_TYPES = 4,
  keep_reference = F,
  cell_type_profiles = NULL,
  CONFIDENCE_THRESHOLD = 5,
  DOUBLET_THRESHOLD = 20
)

Arguments

spatialRNA	a SpatialRNA object to run RCTD on
reference	a Reference object scRNA-seq reference used for RCTD
max_cores	for parallel processing, the number of cores used. If set to 1, parallel processing is not used. The system will additionally be checked for number of available cores.
gene_cutoff	minimum normalized gene expression for genes to be included in the platform effect normalization step.
fc_cutoff	minimum log-fold-change (across cell types) for genes to be included in the platform effect normalization step.
gene_cutoff_reg	minimum normalized gene expression for genes to be included in the RCTD step.
fc_cutoff_reg	minimum log-fold-change (across cell types) for genes to be included in the RCTD step.
UMI_min	minimum UMI per pixel included in the analysis
UMI_max	maximum UMI per pixel included in the analysis
counts_MIN	(default 10) minimum total counts per pixel of genes used in the analysis.
UMI_min_sigma	minimum UMI per pixel for the choose_sigma_c function
class_df	(optional) if not NULL, then a dataframe mapping each cell type to a cell class, so that RCTD will report confidence on the class level.
CELL_MIN_INSTANCE	minimum number of cells required per cell type. Default 25, can be lowered if desired.
cell_type_names	A list of cell types to be included from the reference. If NULL, uses all cell types
MAX_MULTI_TYPES	(multi-mode only) Default 4, max number of cell types per pixel
keep_reference	(Default FALSE) if true, keeps the reference object stored within the RCTD object
cell_type_profiles	Default NULL, option to pass in cell type profiles in directly as a genes by cell type matrix, including gene names and cell type names. If this option is used, reference will be ignored.
CONFIDENCE_THRESHOLD	(Default 5) the minimum change in likelihood (compared to other cell types) necessary to determine a cell type identity with confidence
DOUBLET_THRESHOLD	(Default 20) the penalty weight of predicting a doublet instead of a singlet for a pixel

Value

an RCTD object, which is ready to run the run.RCTD function

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