sizeFactors: Accessors size factors of an SCESet object.

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

For normalisation, library-specific size factors can be defined. Raw values can be divided by the appropriate size factors to obtain normalised counts, TPM, etc.

Usage

## S4 method for signature 'SCESet'
sizeFactors(object,type)

## S4 replacement method for signature 'SCESet,numeric'
sizeFactors(object,type)<-value
## S4 replacement method for signature 'SCESet,NULL'
sizeFactors(object,type)<-value

## S4 method for signature 'SCESet'
sizeFactors(object, type = NULL)

## S4 replacement method for signature 'SCESet,numeric'
sizeFactors(object, type = NULL, ...) <- value

## S4 replacement method for signature 'SCESet,'NULL''
sizeFactors(object, type = NULL, ...) <- value

Arguments

object	a SCESet object.
type	optional character argument providing the type or name of the size factors to be accessed or assigned.
...	further arguments passed to the function
value	a vector of class "numeric" or NULL

Details

The size factors can alternatively be directly accessed from the SCESet object with object$size_factor_type (where "type" in the preceding is replaced by the actual type name).

Value

A numeric vector of size factors.

Author(s)

Davis McCarthy and Aaron Lun

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sceset <- newSCESet(countData = sc_example_counts)
sizeFactors(example_sceset)
sizeFactors(example_sceset, NULL) <- 2 ^ rnorm(ncol(example_sceset))

example_sceset <- calculateQCMetrics(example_sceset,
                                     feature_controls = list(set1 = 1:40))
sizeFactors(example_sceset, "set1") <- 2 ^ rnorm(ncol(example_sceset))
sizeFactors(example_sceset)

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.