run_limma_scseq: Run limma on pseudobulk experiment

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

Run limma on pseudobulk experiment

Description

Run limma on pseudobulk experiment

Usage

run_limma_scseq(
  summed,
  meta,
  species,
  trend = FALSE,
  method = "TMMwsp",
  with_fdata = FALSE,
  progress = NULL,
  value = 0,
  ...
)

Arguments

summed	pseudobulk SingleCellExperiment. If NULL, summed_path must be supplied and the call is assumed to originate from r_bg.
meta	data.frame of sample metadata with column group and row.names set with summed$batch
species	species name used to retrieve feature annotation.
trend	Should limma-trend analysis be run (default is FALSE)? Slightly faster than limma-voom (default). Used for pseudobulk grid differential expression analyses.
method	normalization method to be used.
with_fdata	if TRUE, adds Entrez IDs to fit object which are needed to downstream GO pathway analyses.
progress	progress object or NULL.
value	Initial value of progress.
...	additional arguments to filterByExpr.

Value

List with a fit object, model matrix, and normalized expression matrix.

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