scp_export_clustering_file: scp_export_clustering_file

In amyh25/Rsc: Single Cell Helper Functions

scp_export_clustering_file

Description

Create clustering file for export to the Single Cell Portal https://singlecell.broadinstitute.org/single_cell

Usage

scp_export_clustering_file(
  so,
  str_subset_regex_group = "RNA_snn_res.",
  str_subset_regex_numeric = "_RNA",
  reduction_str = "umap",
  output_dir,
  filename = "clustering_scp"
)

Arguments

so	Seurat object
str_subset_regex_group	regex string to select columns from Seurat object metadata (default: "RNA_snn_res.")
str_subset_regex_numeric	regex string to select columns from Seurat object metadata (default: "_RNA")
reduction_str	string specifying name of reduction. Should match the parameter reduction.name from Seurat::RunUMAP (default: "umap")
output_dir	path to output directory
filename	export filename (default: "clustering_scp")

Value

Seurat object with identity set to given ident

amyh25/Rsc documentation built on Jan. 29, 2024, 7:22 a.m.