runNormalization {singleCellTK} | R Documentation

## Wrapper function to run any of the integrated normalization/transformation methods in the singleCellTK. The available methods include 'LogNormalize', 'CLR', 'RC' and 'SCTransform' from Seurat, 'logNormCounts and 'CPM' from Scater. Additionally, users can 'scale' using Z.Score, 'transform' using log, log1p and sqrt, add 'pseudocounts' and trim the final matrices between a range of values.

### Description

Wrapper function to run any of the integrated normalization/transformation methods in the singleCellTK. The available methods include 'LogNormalize', 'CLR', 'RC' and 'SCTransform' from Seurat, 'logNormCounts and 'CPM' from Scater. Additionally, users can 'scale' using Z.Score, 'transform' using log, log1p and sqrt, add 'pseudocounts' and trim the final matrices between a range of values.

### Usage

    runNormalization(
      inSCE,
      useAssay = "counts",
      outAssayName = "customNormalizedAssay",
      normalizationMethod = NULL,
      scale = FALSE,
      seuratScaleFactor = 10000,
      transformation = NULL,
      pseudocountsBeforeNorm = NULL,
      pseudocountsBeforeTransform = NULL,
      trim = NULL,
      verbose = TRUE
    )

### Arguments

`inSCE` | Input `SingleCellExperiment` object.
`useAssay` | Specify the name of the assay that should be used.
`outAssayName` | Specify the name of the new output assay.
`normalizationMethod` | Specify a normalization method from 'LogNormalize', 'CLR', 'RC' and 'SCTransform' from Seurat or 'logNormCounts' and 'CPM' from scater packages. Default `NULL` is set which will not run any normalization method.
`scale` | Logical value indicating if the data should be scaled using Z.Score. Default `FALSE`.
`seuratScaleFactor` | Specify the 'scaleFactor' argument if a Seurat normalization method is selected. Default is `10000`. This parameter will not be used if methods other than seurat are selected.
`transformation` | Specify the transformation options to run on the selected assay. Options include 'log2' (base 2 log transformation), 'log1p' (natural log + 1 transformation) and 'sqrt' (square root). Default value is `NULL`, which will not run any transformation.
`pseudocountsBeforeNorm` | Specify a numeric pseudo value that should be added to the assay before normalization is performed. Default is `NULL`, which will not add any value.
`pseudocountsBeforeTransform` | Specify a numeric pseudo value that should be added to the assay before transformation is run. Default is `NULL`, which will not add any value.
`trim` | Specify a vector of two numeric values that should be used as the upper and lower trim values to trim the assay between these two values. For example, `c(10,-10)` will trim the values between 10 and -10. Default is `NULL`, which will not trim the data assay.
`verbose` | Logical value indicating if progress messages should be displayed to the user. Default is `TRUE`.

### Value

Output SCE object with new normalized/transformed assay stored.

### Examples

    data(sce_chcl, package = "scds")
    sce_chcl <- runNormalization(
     inSCE = sce_chcl,
     normalizationMethod = "LogNormalize",
     useAssay = "counts",
     outAssayName = "logcounts")

[Package singleCellTK version 2.2.0 Index]