process_seurat_object: Wrapper around Seurat processing functions
In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

process_seurat_object

R Documentation

Wrapper around Seurat processing functions

Description

Wrapper around Seurat processing functions

Usage

process_seurat_object(
  seurat_object,
  assay_name = NULL,
  calculate_rb_and_mt = TRUE,
  remove_stress_and_mt = TRUE,
  SCTransform = FALSE,
  NormalizeData = TRUE,
  FindVariableFeatures = TRUE,
  ScaleData = TRUE,
  RunPCA = TRUE,
  FindNeighbors = TRUE,
  FindClusters = TRUE,
  RunTSNE = TRUE,
  RunUMAP = TRUE,
  verbose = TRUE
)

Arguments

`seurat_object`	A valid seurat-object.
`SCTransform`	A named list of arguments given to `Seurat::SCTransform()`, TRUE or FALSE.
`NormalizeData`	A named list of arguments given to `Seurat::NormalizeData()`, TRUE or FALSE.
`FindVariableFeatures`	A named list of arguments given to `Seurat::FindVariableFeatures()`, TRUE or FALSE.
`ScaleData`	A named list of arguments given to `Seurat::ScaleData()`, TRUE or FALSE. Hint: If set to TRUE or the argument-list provided does not specify the argument `features` input for argument `features` is set to `base::rownames(seurat_object)`.
`RunPCA`	A named list of arguments given to `Seurat::RunPCA()`, TRUE or FALSE.
`FindNeighbors`	A named list of arguments given to `Seurat::FindNeighbors()`, TRUE or FALSE.
`FindClusters`	A named list of arguments given to `Seurat::FindClusters()`, TRUE or FALSE.
`RunTSNE`	A named list of arguments given to `Seurat::RunTSNE()`, TRUE or FALSE.
`RunUMAP`	A named list of arguments given to `Seurat::RunUMAP()`, TRUE or FALSE.
`verbose`	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)