CellDataSet-methods: Methods for the CellDataSet class

Description Usage Arguments

Description

Methods for the CellDataSet class

Usage

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## 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


Bioconductor-mirror/monocle documentation built on Aug. 10, 2017, 10:49 a.m.