Find differentially expressed markers for a MatisseObject

Runs FindMarkers on the embedded Seurat object. Unlike most dispatch methods, this returns a data.frame of marker statistics rather than an updated MatisseObject.

Usage

# S3 method for class 'MatisseObject'
FindMarkers(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  latent.vars = NULL,
  group.by = NULL,
  subset.ident = NULL,
  assay = NULL,
  reduction = NULL,
  ...
)

Arguments

object: A MatisseObject.
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: Variables to test, used only when test.use is one of 'LR', 'negbinom', 'poisson', or 'MAST'
group.by: Regroup cells into a different identity class prior to performing differential expression (see example); "ident" to use Idents
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
reduction: Reduction to use in differential expression testing - will test for DE on cell embeddings
...: Additional arguments forwarded to FindMarkers (e.g. ident.1, ident.2, group.by, features).

Value

A data.frame of marker genes with columns p_val, avg_log2FC, pct.1, pct.2, p_val_adj.

Usage

Arguments

Value

See also