View source: R/perform.seurat.diffexp.all.R
perform.diffexp.all | R Documentation |
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
perform.diffexp.all( object, assay = NULL, clust.method = NULL, column = NULL, test = "wilcox", latent.vars = NULL, ... )
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 |
A dataframe containing differentially expression genes and other information
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')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.