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.

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")
#> Normalization performed using LogNormalize method.