CellDataSet-methods {monocle} | R Documentation |
Methods for the CellDataSet class
## S4 method for signature 'CellDataSet' sizeFactors(object) ## S4 replacement method for signature 'CellDataSet,numeric' sizeFactors(object) <- value ## S4 method for signature 'CellDataSet' estimateSizeFactors(object, locfunc = median, ...) ## S4 method for signature 'CellDataSet' estimateDispersions( object, modelFormulaStr = "~ 1", relative_expr = TRUE, min_cells_detected = 1, remove_outliers = TRUE, cores = 1, ... )
object |
The CellDataSet object |
value |
A vector of size factors, with length equal to the cells in object |
locfunc |
A function applied to the geometric-mean-scaled expression values to derive the size factor. |
... |
Additional arguments to be passed to estimateSizeFactorsForMatrix |
modelFormulaStr |
A model formula, passed as a string, specifying how to group the cells prior to estimated dispersion. The default groups all cells together. |
relative_expr |
Whether to transform expression into relative values |
min_cells_detected |
Only include genes detected above lowerDetectionLimit in at least this many cells in the dispersion calculation |
remove_outliers |
Whether to remove outliers (using Cook's distance) when estimating dispersions |
cores |
The number of cores to use for computing dispersions |