create_seurat_object: Create Seurat object based on sample metadata.

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Create Seurat object based on sample metadata.

Description

This function creates Seurat object for each sample in the metadata file. It also allows the user to perform SoupX (ambient RNA removal) and Scrublet (doublet detection) analysis.

Usage

create_seurat_object(
  data_dir,
  sample_meta = NULL,
  sample_meta_filename = NULL,
  meta_colnames = c("donor", "condition", "pass_qc"),
  plot_dir = NULL,
  use_scrublet = TRUE,
  use_soupx = FALSE,
  tenx_dir = "premrna_outs",
  tenx_counts_dir = "filtered_feature_bc_matrix",
  expected_doublet_rate = 0.06,
  min.cells = 10,
  min.features = 200,
  ...
)

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.
plot_dir	Directory for storing QC plots. Used if use_soupx = TRUE.
use_scrublet	Logical, wether to use Scrublet for doublet detection.
use_soupx	Logical, wether to use SoupX for ambient RNA removal.
tenx_dir	Name of 10x base directory, e.g. with outputs after running cellranger. Default 'premrna_outs', i.e. assumes single-nuclei RNA-seq.
tenx_counts_dir	Name of 10x directory where count matrices are stored. Default 'filtered_feature_bc_matrix'
expected_doublet_rate	The expected fraction of transcriptomes that are doublets, typically 0.05 - 0.1
min.cells	Include features/genes detected in at least this many cells.
min.features	Include cells where at least this many features/genes are detected.
...	Additional named parameters passed to Seurat, Scrublet or SoupX.

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.