runNormalization: Run normalization/transformation with various methods

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Run normalization/transformation with various methods

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 = "logcounts",
  normalizationMethod = "logNormCounts",
  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")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.