RunIntegration: Run Seurat Anchors Integration Pipeline

In Theob0t/scEasyPip: Automated Seurat Pipeline for scRNA-seq analysis

Description

This function integrate a list of Seurat objects using the Seurat Anchors Integration Pipeline and the SCTransform normalization

Usage

RunIntegration(
  rds.list,
  obj.list = NULL,
  output.dir = getwd(),
  resolution = 0.5,
  grouping.var = "orig.ident",
  find.conserved.markers = FALSE,
  ident.1 = NULL,
  ident.2 = NULL,
  save.rds = TRUE,
  ...
)

Arguments

rds.list	A vector of rds files paths
obj.list	A vector of Seurat objects
output.dir	Path to the destination folder of saved files
resolution	Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.
grouping.var	grouping variable
find.conserved.markers	Run FindConservedMarkers (default set to False)
ident.1	Identity class to define markers for
ident.2	A second identity class for comparison. If NULL (default) - use all other cells for comparison.
save.rds	Save final Seurat object in RDS format (default set to True)
...	Arguments passed to as.sparse

Value

An integrated Seurat Object along with its visualization plots

Theob0t/scEasyPip documentation built on Dec. 18, 2021, 4:10 p.m.