CellDataSet-methods {monocle} | R Documentation

## Methods for the CellDataSet class

### Description

Methods for the CellDataSet class

### Usage

    ## 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,
      ...
    )

### Arguments

`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

[Package monocle version 2.22.0 Index]