Perform differential expression — perform.diffexp • IBRAP

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(
  object,
  assay = NULL,
  test = "wilcox",
  identity = NULL,
  ident.1 = NULL,
  ident.2 = NULL,
  cells.1 = NULL,
  cells.2 = NULL,
  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.
identity: Vector. A vector of cell identifiers to distinguish cells. Default = NULL
latent.vars: Character. String(s) identifying which variables contained within the metadata to regress from the cells
...: arguments to pass to Seurat::FindMarkers

Value

A dataframe containing differentially expression genes and other information