spatial_create_seurat_object: Create Seurat object based on spatial sample metadata.

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Create Seurat object based on spatial sample metadata.

Description

This function creates Seurat object for each spatial (e.g. Visium) sample in the metadata file.

Usage

spatial_create_seurat_object(
  data_dir,
  sample_meta = NULL,
  sample_meta_filename = NULL,
  meta_colnames = c("donor", "condition", "pass_qc"),
  tenx_dir = "outs",
  ...
)

Arguments

data_dir	Parent directory where all sample 10x files are stored. Think of it as project directory.
sample_meta	Sample metadata information in a Data.frame like object. Columns should at least contain 'sample', 'donor', 'condition' and 'pass_qc'.
sample_meta_filename	Filename of sample metadata information, same as 'meta' parameter above. User should provide one of 'meta' or 'meta_filename'.
meta_colnames	Sample metadata column names to store in Seurat metadata.
tenx_dir	Name of 10x base directory, e.g. with outputs after running cellranger. Default 'premrna_outs', i.e. assumes single-nuclei RNA-seq.
...	Additional named parameters passed to Seurat.

Value

List of Seurat objects equal the number of samples in the sample metadata file. If a single sample, returns a Seurat object.

Author(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.