CSIDE.population.inference: Runs population-level differential expression inference for a...

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

Runs population-level differential expression inference for a RCTD.replicates object

Description

First, CSIDE must have been run on all replicates using e.g. the run.CSIDE.replicates function.

Usage

CSIDE.population.inference(
  RCTD.replicates,
  params_to_test = NULL,
  use.groups = FALSE,
  MIN.CONV.REPLICATES = 2,
  MIN.CONV.GROUPS = 2,
  CT.PROP = 0.5,
  fdr = 0.01,
  log_fc_thresh = 0.4,
  normalize_expr = F,
  meta = FALSE,
  meta.design.matrix = NULL,
  meta.test_var = "intrcpt"
)

Arguments

RCTD.replicates	a RCTD.replicates object for which to perform population-level DE inference. Note, at least three replicates must be provided.
use.groups	(default FALSE) if TRUE, treats the replicates as having multiple groups (e.g. samples) according to the group_ids slot
MIN.CONV.REPLICATES	(default 2) the minimum number of replicates (if not use.groups) for which a gene must converge
MIN.CONV.GROUPS	(default 2) the minimum number of groups (if use.groups) for which a gene must converge
CT.PROP	(default 0.5) minimum ratio of gene expression within cell type compared to other cell types
fdr	(default 0.01) false discovery rate
log_fc_thresh	(default 0.4) minimum natural log estimated DE threshold
normalize_expr	(default FALSE) if TRUE, constrains total gene expression to sum to 1 in each condition
meta	(default FALSE) if TRUE, conducts population inference using general meta regression
meta.design.matrix	(default NULL) if meta == TRUE, then this is the design matrix for meta regression. Rows are samples and named columns are covariates.
meta.test_var	(default 'intrcpt') if meta == TRUE, this indicates which variable is tested in the meta regression. By default the intercept is tested, but one can also test for fixed effects of other covariates.
params_to_test:	(default 2 for test_mode = 'individual', all parameters for test_mode = 'categorical'). An integer vector of parameter indices to test. Note, for population mode, only the first parameter is tested.

Value

an RCTD.replicates object containing the results of the CSIDE population-level algorithm. See RCTD.replicates for documentation on the population_de_results, population_sig_gene_list, and population_sig_gene_df objects.

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