runScanorama: Integrate scRNA-seq data using Scanorama

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Integrate scRNA-seq data using Scanorama

Description

This is a wrapper for Scanorama (https://github.com/brianhie/scanorama). Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets.

Usage

runScanorama(
  object,
  batch,
  do.umap = F,
  nfeatures = 2000,
  vars2regress = "percent.mt",
  dim = 50L,
  verbose = T
)

Arguments

object	Seurat object or list of seurat objects.
batch	name of meta data field specifying batch groupings.
do.umap	compute UMAP. Default is T.
nfeatures	number of features to use for integration. Default is 2000.
vars2regress	variable to regress out. Ignored if SCT assay is available in provided object.
dim	number of dimensions to use for integration. Default is 50L.
verbose	print progress. Default is T.

Value

Seurat object.

Author(s)

Nicholas Mikolajewicz

Examples

 object <- runScanorama(object, batch = "sample")

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.