get_de_genes: Returns a list of differentially expressed genes

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

Returns a list of differentially expressed genes

Description

For each cell type, chooses genes that have a minimum average normalized expression in that cell type, and whose expression is larger in that cell type than the average of all cell types. Filters out mitochondrial genes.

Usage

get_de_genes(
  cell_type_info,
  puck,
  fc_thresh = 1.25,
  expr_thresh = 0.00015,
  MIN_OBS = 3
)

Arguments

cell_type_info	cell type information and profiles of each cell, calculated from the scRNA-seq reference (see get_cell_type_info)
puck	an object of type SpatialRNA
fc_thresh	minimum log_e fold change required for a gene.
expr_thresh	minimum expression threshold, as normalized expression (proportion out of 1, or counts per 1).
MIN_OBS	the minimum number of occurances of each gene in the SpatialRNA object.

Value

a list of differntially expressed gene names

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