RunPrestoAll: A Presto-based implementation of FindAllMarkers that runs...

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

A Presto-based implementation of FindAllMarkers that runs Wilcoxon tests for all identity classes

Description

Finds markers (Wilcoxon-differentially expressed genes) for each of the identity classes in a dataset

Usage

RunPrestoAll(
  object,
  assay = NULL,
  features = NULL,
  logfc.threshold = 0.25,
  test.use = "wilcox",
  slot = "data",
  min.pct = 0.1,
  min.diff.pct = -Inf,
  node = NULL,
  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,
  return.thresh = 0.01,
  ...
)

Arguments

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"
node	A node to find markers for and all its children; requires BuildClusterTree to have been run previously; replaces FindAllMarkersNode
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.
return.thresh	Only return markers that have a p-value < return.thresh, or a power > return.thresh (if the test is ROC)

Value

Matrix containing a ranked list of putative markers, and associated statistics (p-values, logFC, etc.)

See Also

https://github.com/immunogenomics/presto

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