NormalizeAndScale: Run the primary seurat processing steps.

View source: R/Seurat_III.R

NormalizeAndScaleR Documentation

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.