processSeurat: Pipes together several downstream Seurat steps including...

In basilkhuder/extendSC: Extends functionalities of scRNA-Seq workflows

Description

Pipes together several downstream Seurat steps including variance-stabilizing transformation, PCA, clustering and nonlinear dimensionality reduction

Usage

processSeurat(
  seurat.obj,
  dims = 1:50,
  cluster.res = 0.2,
  vars_to_regress = c("orig.ident", "percent.mt"),
  seed.use = 24,
  n.cores = NULL
)

Arguments

seurat.obj	A seurat object.
dims	Dimensions of reduction to use as input for FindNeighbors and RunUMAP
cluster.res	Cluster resolution for FindClusters
vars_to_regress	Variables to regress out in a second non-regularized linear regression for SCTransform
seed.use	Seed to set for RunUMAP
n.cores	Number of cores to use

Value

A processed Seurat object

Examples

processSeurat(seurat.obj, dims = 1:50, cluster.res = .2, vars_to_regress = c("orig.ident","percent.mt"))

basilkhuder/extendSC documentation built on July 23, 2021, 1:17 p.m.