findMastMarkers_one_vs_all#

Last Updated: Oct 02, 2023

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