RunPresto: A Presto-based implementation of FindMarkers that runs...

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

A Presto-based implementation of FindMarkers that runs Wilcoxon tests for the given identity classes

Description

A Presto-based implementation of FindMarkers that runs Wilcoxon tests for the given identity classes

Usage

RunPresto(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  group.by = NULL,
  subset.ident = NULL,
  assay = NULL,
  slot = "data",
  reduction = NULL,
  features = NULL,
  logfc.threshold = 0.25,
  test.use = "wilcox",
  min.pct = 0.1,
  min.diff.pct = -Inf,
  verbose = TRUE,
  only.pos = FALSE,
  max.cells.per.ident = Inf,
  random.seed = 1,
  latent.vars = NULL,
  min.cells.feature = 3,
  min.cells.group = 3,
  mean.fxn = NULL,
  fc.name = NULL,
  base = 2,
  ...
)

Arguments

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
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
slot	Slot to pull data from; note that if test.use is "negbinom", "poisson", or "DESeq2", slot will be set to "counts"
reduction	Reduction to use in differential expression testing - will test for DE on cell embeddings
mean.fxn	Function to use for fold change or average difference calculation. If NULL, the appropriate function will be chose according to the slot used
fc.name	Name of the fold change, average difference, or custom function column in the output data.frame. If NULL, the fold change column will be named according to the logarithm base (eg, "avg_log2FC"), or if using the scale.data slot "avg_diff".
base	The base with respect to which logarithms are computed.

See Also

https://github.com/immunogenomics/presto

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.