CellDataSet-methods: Methods for the CellDataSet class

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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

monocle documentation built on Nov. 8, 2020, 5:06 p.m.