DLG.get.param: DLG.get.param

In livnatje/DIALOGUE: DIALOGUE is a dimensionality reduction algorithm that uses cross-cell-type associations to identify multicellular programs and map the cell transcriptome as a function of its environment.

DLG.get.param

Description

DIALOGUE is a dimensionality reduction approach that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

Usage

DLG.get.param(
  k = 2,
  results.dir = DLG.file("/Results/MCPs/"),
  seed1 = 1234,
  plot.flag = F,
  penalty = NULL,
  MCP.cell.types = NULL,
  frm = NULL,
  pheno = NULL,
  PMD2 = F,
  single.BH = F,
  extra.sparse = F,
  abn.c = 15,
  conf = "cellQ",
  covar = c("cellQ", "tme.qc"),
  n.genes = 200,
  averaging.function = colMedians,
  p.anova = 0.05,
  find.genes = T,
  specific.pair = NULL,
  center.flag = T,
  bypass.emp = F,
  parallel.vs = F,
  spatial.flag = F,
  full.version = T
)

Arguments

k	the number of multicellular programs to identify;
results.dir	path to the results directory, where the output will be saved;
plot.flag	if TRUE then DIALOGUE.plot will be called to plot the results; default is FALSE;
abn.c	the minimal number of cells that a sample should have to be considered for MCP detection;
spatial.flag	should be TRUE if working with spatial data with small niches, and TRUE if working with single cell data or larger tissue microenvironment niches. The default value is FALSE.

Value

A list with the parameters as input for DIALOGUE.run

Author(s)

Livnat Jerby

See Also

See DIALOGUE GitHub page for more details. DIALOGUE.plot

livnatje/DIALOGUE documentation built on Jan. 30, 2024, 1:31 a.m.