results: results

In rhondabacher/SCnorm: Normalization of single cell RNA-seq data

results

Description

Convenient helper function to extract the results ( normalized data, list of genes filtered out, or scale factors). Results data.frames/matrices are stored in the metadata slot and can also be accessed without the help of this convenience function by calling metadata(DataNorm).

Usage

results(DATA, type = c("NormalizedData", "ScaleFactors", "GenesFilteredOut"))

Arguments

DATA

An object of class SummarizedExperiment that contains normalized single-cell expression and other metadata, and the output of the SCnorm function.

type

A character variable specifying which output is desired, with possible values "NormalizedData", "ScaleFactors", and "GenesFilteredOut". By default results() will return type="NormalizedData", which is the matrix of normalized counts from SCnorm. By specifiying type="ScaleFactors" a matrix of scale factors (only returned if reportSF=TRUE when running SCnorm()) can be obtained. type="GenesFilteredOut" returns a list of genes that were not normalized using SCnorm, these are genes that did not pass the filter critiera.

Value

A data.frame containing output as detailed in the description of the type input parameter

Examples

data(ExampleSimSCData)
Conditions = rep(c(1), each= 90)
#NormData <- SCnorm(Data=ExampleSimSCData, Conditions=Conditions)
#normDataMatrix <- results(NormData)

rhondabacher/SCnorm documentation built on July 8, 2023, 11:36 p.m.