R/srcLineagePulse_calcNormConst.R

In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#+++++++++++++++++++++++     Compute Size factors    +++++++++++++++++++++++++#
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#

#' Compute size factors for a LineagePulse-object
#' 
#' Either use externally supplied normalisation constants or set these to one.
#' 
#' @seealso Called by \code{runLineagePulse}.
#' 
#' @param objLP (LineagePulse-object)
#' Object to fit normalization constants on.
#' @param vecNormConstExternal (numeric vector number of cells) 
#' Model scaling factors supplied by user, one per cell. 
#' 
#' @return objLP (LineagePulse-object)
#' Object with fit normalization constants.
#' 
#' @author David Sebastian Fischer
calcNormConst <- function(objLP,
                          vecNormConstExternal){
    
    if(!is.null(vecNormConstExternal)){
        vecNormConst <- vecNormConstExternal
    } else {
        message("# All size factors are set to one.")
        vecNormConst <- array(1, dim(matCountsProc(objLP))[2])
        names(vecNormConst) <- colnames(matCountsProc(objLP))
    }
    
    if(any(vecNormConst==0)){
        warning("WARNING IN LINEAGEPULSE: Found size factors==0.",
                " Setting these to 1.")
        vecNormConst[vecNormConst==0] <- 1
    }
    
    return(as.vector(vecNormConst))
}