createSeuratObjectPipeline: Creates Seurat object from 10X cell ranger output

In kimberle9/rfca: Random Forest Cell Annotation of single-cell transcriptomics data

Description

Creates Seurat object from 10X cell ranger output

Usage

createSeuratObjectPipeline(
  data.dir = "~/filtered_feature_bc_matrix",
  nFeature_RNA_lower = 500,
  nFeature_RNA_upper = 5000,
  percent.mt = 5,
  nfeatures = 2000,
  dims = 20,
  clusterResolution = 0.8
)

Arguments

data.dir	Directory where data is stored. Default "~/filtered_feature_bc_matrix".
nFeature_RNA_lower	Lower bound of nFeature_RNA. Default 500.
nFeature_RNA_upper	Upper bound of nFeature_RNA. Default 5000.
percent.mt	Upper bound of percentage of mitochondria genes. Default 5.
nfeatures	Number of top most variable genes. Default 2000.
dims	Number of dimensions for finding neighbors and UMAP. Default 20.
clusterResolution	Cluster resolution for finding clusters. Default 0.8.

Value

Seurat Object with pca and UMAP calculated, ready for use with predictCells().

Author(s)

Kimberle Shen

kimberle9/rfca documentation built on Oct. 8, 2020, 5:44 a.m.