results {SCnorm} | R Documentation

## 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)

[Package SCnorm version 1.9.1 Index]