Differential test with PACS on Seurat object

Run differential test using the similar style as in Seurat Seurat::FindMarkers() function. Note 1: This function is modified from Seurat package v5.1.0 Note 2: Seurat must be installed to use this function.

Usage

FindMarkersPACS(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  latent.vars = NULL,
  group.by = NULL,
  subset.ident = NULL,
  assay = "count",
  reduction = NULL,
  ...
)

Arguments

object: A Seurat object
ident.1: Identity class to define markers for; pass an object of class phylo or 'clustertree' to find markers for a node in a cluster tree; passing 'clustertree' requires BuildClusterTree to have been run
ident.2: A second identity class for comparison; if NULL, use all other cells for comparison; if an object of class phylo or 'clustertree' is passed to ident.1, must pass a node to find markers for
latent.vars: Latent variables to be controlled for from the meta.data column of the Seurat object
group.by: Regroup cells into a different identity class prior to performing differential expression (see example)
subset.ident: Subset a particular identity class prior to regrouping. Only relevant if group.by is set (see example)
assay: Assay to use in differential expression testing, for PACS, we use count as assay
reduction: Reduction to use in differential expression testing - will test for DE on cell embeddings
...: Additional arguments for identifying differential peaks