RunBasicSeurat: Run Standard Seurat Pipeline

In huayc09/SeuratExtend: SeuratExtend

Run Standard Seurat Pipeline

Description

This function processes a Seurat object through various steps including normalization, PCA, and clustering based on specified parameters. It allows for conditional execution of each step based on prior executions and parameter changes.

Usage

RunBasicSeurat(
  seu,
  spe = NULL,
  nFeature_RNA.min = 500,
  nFeature_RNA.max = Inf,
  percent.mt.max = 20,
  dims = 1:10,
  resolution = 0.5,
  reduction = NULL,
  harmony.by = NULL,
  force.Normalize = FALSE,
  force.RunPCA = FALSE,
  vars.to.regress = NULL,
  force.RunHarmony = FALSE,
  force.FindNeighbors = FALSE,
  force.FindClusters = FALSE,
  force.RunUMAP = FALSE
)

Arguments

seu	A Seurat object that will be processed.
spe	Either "human" or "mouse", used in calculating percent.mt. Default: NULL.
nFeature_RNA.min	The minimum number of RNA features to include in the subset. Default: 500.
nFeature_RNA.max	The maximum number of RNA features to include in the subset. Default: Inf.
percent.mt.max	The maximum percentage of mitochondrial content allowed for cells in the subset. Default: 20.
dims	The dimensions to be used in RunPCA and FindNeighbors. Default: 1:10.
resolution	The resolution parameter for the clustering algorithm. Default: 0.5.
reduction	The dimensional reduction technique to be used ('pca' or 'harmony'). If NULL, the method is determined based on available data in the Seurat object. Default: NULL.
harmony.by	A string representing a metadata column in the Seurat object that categorizes data, which might need transformation for numeric-only issues before running Harmony. Default: NULL.
force.Normalize	Forces the normalization step regardless of previous command history. Default: FALSE.
force.RunPCA	Forces the PCA step regardless of previous command history. Default: FALSE.
vars.to.regress	Variables to regress out during scaling. Default: NULL.
force.RunHarmony	Forces the Harmony integration step regardless of previous command history or detection. Default: FALSE.
force.FindNeighbors	Forces the neighbor finding step regardless of previous command history. Default: FALSE.
force.FindClusters	Forces the clustering step regardless of previous command history. Default: FALSE.
force.RunUMAP	Forces the UMAP step regardless of previous command history. Default: FALSE.

Details

This function provides flexible and conditional execution of various data processing steps in a Seurat pipeline. Depending on the parameters set, the function intelligently determines whether to rerun specific steps based on changes in parameters or previous runs recorded in the Seurat object's command history. This allows for efficient reuse of existing results while ensuring updates are applied when necessary.

Value

Returns the modified Seurat object after performing the requested operations and updates.

Examples

library(SeuratExtend)
pbmc <- RunBasicSeurat(pbmc, force.Normalize = TRUE)
DimPlot2(pbmc, group.by = "cluster")

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.