DIALOGUE.run: DIALOGUE.run

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.

DIALOGUE.run

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

DIALOGUE.run(rA, main, param, plot.flag = T)

Arguments

rA	list of cell.type objects.
main	the name of the run that will be used for naming the output files in the results directory
param	the parameters of the run - these will also be saved with the output for reproducibility. See DLG.get.param for more information.
plot.flag	if TRUE then DIALOGUE.plot will be called to plot the results; default is FALSE;

Value

A list with the following components:

sig - the multicellular programs, given as a list of signatures;

scores - the multicellular programs' scores in each cell;

gene.pval - the cross-cell-type p-values of each program;

pref - the correlation (R) and association (mixed-effects p-value) between the cell-type-sepcific components of each multicellular programs.

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.