load_stellarscope_seurat: Load count matrix from Stellarscope output files

In nixonlab/scopetools: What the Package Does (One Line, Title Case)

Load count matrix from Stellarscope output files

Description

This returns a Seurat object with raw counts from Stellarscope and STARsolo (if provided). Only cell barcodes present in both are retained. Feature metadata can also be included for TEs and genes.

Usage

load_stellarscope_seurat(
  stellarscope_dir,
  starsolo_dir = NULL,
  exp_tag = "stellarscope",
  project = "StellarscopeProject",
  min.cells = 0,
  min.features = 0,
  remove.nofeat = TRUE,
  TE_count_filename = "*TE_counts.mtx",
  TE_feature_filename = "*features.tsv",
  TE_barcode_filename = "*barcodes.tsv",
  GENE_count_filename = "*matrix.mtx",
  GENE_feature_filename = "*features.tsv",
  GENE_barcode_filename = "*barcodes.tsv",
  TE_metadata = data.frame(retro.hg38.v1, row.names = "locus"),
  GE_metadata = NULL,
  use.symbols = TRUE
)

Arguments

stellarscope_dir	Stellarscope output directory
starsolo_dir	STARsolo output directory, optional.
exp_tag	Experiment tag used in stellarscope run. Default is "stellarscope".
project	Project name for the Seurat object
min.cells	Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
min.features	Include cells where at least this many features are detected.
remove.nofeat	Remove "no feature" category from Stellarscope counts. Default is TRUE.
TE_count_filename	File name pattern for TE count matrix (MTX format). May contain wildcards.Default is '*TE_counts.mtx'.
TE_feature_filename	File name pattern for TE feature list (tab-separated, features in first column). May contain wildcards. Default is '*features.tsv'.
TE_barcode_filename	File name pattern for TE barcode list (tab-separated, barcodes in first column). May contain wildcards. Default is '*barcodes.tsv'.
GENE_count_filename	File name pattern for gene count matrix (MTX format). May contain wildcards. Default is '*matrix.mtx'.
GENE_feature_filename	File name pattern for gene feature list (tab-separated, features in first column). May contain wildcards. Default is '*features.tsv'.
GENE_barcode_filename	File name pattern for gene barcode list (tab-separated, barcodes in first column). May contain wildcards. Default is '*barcodes.tsv'.
TE_metadata	Data frame with metadata related to the TE features
GE_metadata	Data frame with metadata related to the gene features
use.symbols	Use gene symbols as the gene ID. Duplicate symbols have sequential numbers appended (using base::make.unique()). Default is TRUE.

Value

A Seurat object with counts from stellarscope and STARsolo.

See Also

base::make.unique() for use.symbols

nixonlab/scopetools documentation built on Sept. 30, 2022, 11:15 a.m.