NormalizeAndScale: Run the primary seurat processing steps.

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Run the primary seurat processing steps.

Description

This is the primary entry point for processing scRNAseq data with Seurat

Usage

NormalizeAndScale(
  seuratObj,
  nVariableFeatures = NULL,
  block.size = 1000,
  variableGenesWhitelist = NULL,
  variableGenesBlacklist = NULL,
  featuresToRegress = c(paste0("nCount_", Seurat::DefaultAssay(seuratObj))),
  scaleVariableFeaturesOnly = TRUE,
  includeCellCycleGenesInScaleData = TRUE,
  useSCTransform = FALSE,
  additionalFindVariableFeatureArgList = NULL,
  scoreCellCycle = TRUE,
  useAlternateG2M = FALSE
)

Arguments

seuratObj	A Seurat object.
nVariableFeatures	The number of variable features, passed to either FindVariableFeatures or SCTransform
block.size	Passed directly to ScaleData
variableGenesWhitelist	An optional vector of genes that will be included in PCA, beyond the default VariableFeatures()
variableGenesBlacklist	An optional vector of genes that will be excluded from PCA, beyond the default VariableFeatures()
featuresToRegress	The set of features which will be passed to Seurat::ScaleData vars.to.regress
scaleVariableFeaturesOnly	If true, ScaleData will only be performed on VariableFeatures(), which is governed by FindVariableFeatures, variableGenesWhitelist, and variableGenesBlacklist
includeCellCycleGenesInScaleData	If true, cell cycle genes will always be included in the features passed to ScaleData().
useSCTransform	If true, SCTransform will be used in place of the standard Seurat workflow (NormalizeData, ScaleData, FindVariableFeatures)
additionalFindVariableFeatureArgList	A list of arguments passed directly to FindVariableFeatures
scoreCellCycle	If true, ScoreCellCycle will be run to compute Phase, which is stored in meta.data. If a field named Phase already exists, this will be skipped.
useAlternateG2M	If true, this will use a smaller set of G2M genes, defined from: https://raw.githubusercontent.com/hbc/tinyatlas/master/cell_cycle/Homo_sapiens.csv

Value

A modified Seurat object.

bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.