findMastMarkers_one_vs_all: findMastMarkers_one_vs_all

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Identify marker genes for all clusters in a one vs all manner based on the MAST package.

Usage

findMastMarkers_one_vs_all(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  adjust_columns = NULL,
  pval = 0.001,
  logFC = 1,
  min_genes = 10,
  verbose = TRUE,
  ...
)

Arguments

gobject	giotto object
expression_values	gene expression values to use
cluster_column	clusters to use
subset_clusters	selection of clusters to compare
adjust_columns	column in pDataDT to adjust for (e.g. detection rate)
pval	filter on minimal p-value
logFC	filter on logFC
min_genes	minimum genes to keep per cluster, overrides pval and logFC
verbose	be verbose
...	additional parameters for the zlm function in MAST

Value

data.table with marker genes

See Also

findMastMarkers

Examples

    findMastMarkers_one_vs_all(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.