R/runCorrelation.R

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

#' @title runCorrelation
#' @description Calculates the spearman correlation on the input expression matrix & saves the results in SCENIC format
#' @param exprMat_filtered Expression matrix (filtered)
#' @param scenicOptions Fields used: Intermediate file name "corrMat"
#' @return Writes the output in the file name stored in: \code{getIntName(scenicOptions, "corrMat")}
#' @examples 
#' library(SCENIC)
#' scenicOptions <- readRDS("int/scenicOptions.Rds")
#' 
#' loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom")
#' exprMat <- SCopeLoomR::get_dgem(SCopeLoomR::open_loom(loomPath))
#' 
#' genesKept <- loadInt(scenicOptions, "genesKept")
#' exprMatrix_filtered <- exprMat[genesKept,]
#' exprMat_filtered <- log2(exprMatrix_filtered+1) 
#' 
#' runCorrelation(exprMat_filtered, scenicOptions)
#' @export 
runCorrelation <- function(exprMat_filtered,scenicOptions)
{
  corrMat <- cor(t(exprMat_filtered), method="spearman")
  saveRDS(corrMat, file=getIntName(scenicOptions, "corrMat"))
}