determine.background.to.remove error in readme

[CebolaLab]

Hi,

I think the suggested command on your readme page may have an error? It reads:

ambientProfile = determine.background.to.remove(fullMatrix, cellMatrix, emptyDropletCutoff, contaminationChanceCutoff)
cellMatrix     = remove.background(cellMatrix, ambientProfile)

Yet when I look at the determine.background.to.remove function, I see:

function (fullCellMatrix, emptyDropletCutoff, contaminationChanceCutoff) 
{
    backGroundMax = as.vector(qlcMatrix::rowMax(fullCellMatrix[, 
        Matrix::colSums(fullCellMatrix) < emptyDropletCutoff]))
    names(backGroundMax) = rownames(fullCellMatrix)
    nEmpty = table((Matrix::colSums(fullCellMatrix) < emptyDropletCutoff) & 
        (Matrix::colSums(fullCellMatrix) > 0))[2]
    occurences = Matrix::rowSums(fullCellMatrix[, Matrix::colSums(fullCellMatrix) < 
        emptyDropletCutoff] != 0)
    probabiltyCellContaminationPerGene = occurences/nEmpty
    backGroundMax[probabiltyCellContaminationPerGene < contaminationChanceCutoff] = 0
    return(backGroundMax)
}

Which does not have cellMatrix as an input?

[EYNOCATTFOS]

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