R/beadLevelData_setWeights.R

In markdunning/beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

setWeights = function(BLData, wts, array, combine = FALSE, wtName = "wts"){

    if (length(array) == 1)
    {
        ##one array
        if(combine)
        {
            #check for existing weights
            if(!wtName %in% colnames(BLData[[array]]))
            {
                ##Try and insert the weights into the beadLevelData

                BLData = insertBeadData(BLData, array=array, what=wtName, data = wts)
            }
            else
            {
                wtCol = grep(wtName, colnames(BLData[[array]]))

                ##Try and insert the weights into the beadLevelData

                if(length(wtCol) > 0) combinedWts = pmin(wts,BLData[[array]][,wtCol])
                else combinedWts = wts

                BLData = insertBeadData(BLData, array=array, what=wtName,data = combinedWts)
            }
        }
        else
        {
            BLData = insertBeadData(BLData, array=array, what=wtName, data = wts)
        }
    }
    else
    {
            ##multiple arrays
            if(combine)
            {
                    for(i in array)
                    {
                            #check for existing weights
                            if(!wtName %in% colnames(BLData[[array]]))
                            {BLData = insertBeadData(BLData, array=i, what=wtName, data = wts[[i]])}
                            else{
                                    wtCol = grep(wtName, colnames(BLData[[array]]))

                                    if(length(wtCol) > 0) combinedWts = pmin(wts,BLData[[array]][,wtCol])
                                    else combinedWts = wts

                                    BLData = insertBeadData(BLData, array=i, what=wtName, data = combinedWts)
                            }
                    }		
            }
            else
            {
                    for(i in array)
                    {
                            BLData = insertBeadData(BLData, array=i, what=wtName, data = wts[[i]])
                    }
            }
    }

    return(BLData)

}