`findScranMarkers_one_vs_all`¶

findScranMarkers_one_vs_all

Description¶

Identify marker feats for all clusters in a one vs all manner based on scran’s implementation of findMarkers.

Usage¶

findScranMarkers_one_vs_all(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  pval = 0.01,
  logFC = 0.5,
  min_feats = 10,
  min_genes = NULL,
  verbose = TRUE,
  ...
)

Arguments¶

Argument	Description
`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`expression_values`	feat expression values to use
`cluster_column`	clusters to use
`subset_clusters`	subset of clusters to use
`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 findMarkers function in scran

Value¶

data.table with marker feats

Seealso¶

``findScranMarkers` <#findscranmarkers>`_