perform.diffexp.all: Perform differential expression one cluster vs all

In connorhknight/IBRAP_no_decontX: Integrated Benchmarking scRNA-seq Analytical Pipeline

Description

Performs differential expression on the assay differentiating the supplied identities, some methods enable variable regression, including: LR, negbinom, poisson or MAST. This function compares one cluster vs all others

Usage

perform.diffexp.all(
  object,
  assay = NULL,
  clust.method = NULL,
  column = NULL,
  test = "wilcox",
  latent.vars = NULL,
  ...
)

Arguments

object	An IBRAP class object
assay	Character. Which assay within the IBRAP object to access. Default = NULL
test	Character. Which test to use. Can be either: wilcox, bimod, roc, t, negbinom, poisson, LR, MAST, DESeq2. Please refer to Seurat::FindMarkers for more information.
latent.vars	Character. String(s) identifying which variables contained within the metadata to regress from the cells
...	arguments to pass to Seurat::FindMarkers
identity	Vector. A vector of cell identifiers to distinguish cells. Default = NULL

Value

A dataframe containing differentially expression genes and other information

Examples

SCT_DE <- perform.seurat.diffexp.all(object = object, 
                                     assay = 'SCT', 
                                     test = 'MAST', 
                                     identity = object@sample_metadata$celltype, 
                                     latent.vars = 'original.project')
                                     
SCRAN_DE <- perform.seurat.diffexp.all(object = object, 
                                       assay = 'SCRAN', 
                                       test = 'MAST', 
                                       identity = object@sample_metadata$celltype, 
                                       latent.vars = 'original.project')
                                       
SCANPY_DE <- perform.seurat.diffexp.all(object = object, 
                                        assay = 'SCRAN', 
                                        test = 'MAST', 
                                        identity = object@sample_metadata$celltype, 
                                        latent.vars = 'original.project')

connorhknight/IBRAP_no_decontX documentation built on Feb. 13, 2022, 2:32 p.m.