load_scseq_qs: Load SingleCellExperiment from qs file

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Load SingleCellExperiment from qs file

Description

Also attaches clusters from last applied leiden resolution and stores resolution.

Usage

load_scseq_qs(
  dataset_dir,
  meta = NULL,
  groups = NULL,
  with_logs = FALSE,
  with_counts = FALSE
)

Arguments

dataset_dir	Path to folder with scseq.qs file
meta	data.frame with column group and row.names as sample names corresponding to scseq$batch. Default (NULL) loads previous specification from file.
groups	character vector of length two. First value is test group name and second in control group name.
with_logs	should logcounts be loaded? Default is FALSE to increase speed and reduce memory usage.
with_counts	should counts be loaded? Default is FALSE to increase speed and reduce memory usage.

Value

SingleCellExperiment

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.