findMastMarkers_one_vs_all: findMastMarkers_one_vs_all

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

findMastMarkers_one_vs_all

Description

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

Usage

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

Arguments

gobject	giotto object
feat_type	feature type
spat_unit	spatial unit
expression_values	feat 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_feats	minimum feats to keep per cluster, overrides pval and logFC
min_genes	deprecated, use min_feats
verbose	be verbose
...	additional parameters for the zlm function in MAST

Value

data.table with marker feats

See Also

findMastMarkers

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.