Definitions for arguments in `DIALOGUE.run`

[bmill3r]

Hello,

I'm looking through the arguments in DIALOGUE.run to make sure that I am applying the tool properly but i noticed that some of the arguments are not defined. Can you please specify what each of the different arguments do?

#' DIALOGUE.run
#'
#' 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. 
#' 
#' @param rA list of \linkS4class{cell.type} objects.
#' @param k the number of multicellular programs to identify;
#' @param results.dir path to the results directory, where the output will be saved;
#' @param plot.flag if TRUE then \code{\link{DIALOGUE.plot}} will be called to plot the results; default is FALSE;
#' @param abn.c the minimal number of cells that a sample should have to be considered for MCP detection;
#' @param 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.
#' @param add.effects whether to add additional covariates to the multilevel model;
#' if TRUE then the covariates will extracted from the [conf] slot in the \linkS4class{cell.type} objects;
#' default is FALSE.
#' 
#' @return A list with the following components:
#' @return sig -  the multicellular programs, given as a list of signatures;
#' @return scores - the multicellular programs' scores in each cell;
#' @return gene.pval - the cross-cell-type p-values of each program;
#' @return pref - the correlation (R) and association (mixed-effects p-value) between the cell-type-sepcific
#' components of each multicellular programs.
#' @seealso See \href{https://github.com/livnatje/DIALOGUE}{DIALOGUE GitHub page} for more details.
#' \code{\link{DIALOGUE.plot}}
#' @author Livnat Jerby-Arnon
#' @export
#' 

DIALOGUE.run<-function(rA,main,k = 3,results.dir = getwd(),plot.flag = T,pheno = NULL,
                       PMD2 = F,conf = "cellQ",covar = c("cellQ","tme.qc"),n.genes = 200,
                       averaging.function = colMedians,p.anova = 0.05,specific.pair = NULL,
                       parallel.vs = F,center.flag = T,extra.sparse = F, bypass.emp = F, abn.c = 15, spatial.flag = F)

For example, not sure what PMD2, conf, covar, n.genes, averaging.function, p.anova, specific.pair, parallel.vs, center.flag, extra.sparse, bypass.emp, or spatial.flag are specifically doing or what their purposes are.

Also, for the pheno argument, how would one specify a phenotype of interest, presumably within the cell.type object rA?

Thanks, Brendan