findGiniMarkers_one_vs_all#

Last Updated: Oct 02, 2023

Description#

Identify marker feats for all clusters in a one vs all manner based on gini detection and expression scores.

Usage#

findGiniMarkers_one_vs_all(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  min_expr_gini_score = 0.5,
  min_det_gini_score = 0.5,
  detection_threshold = 0,
  rank_score = 1,
  min_feats = 4,
  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
`min_expr_gini_score`	filter on minimum gini coefficient on expression
`min_det_gini_score`	filter on minimum gini coefficient on detection
`detection_threshold`	detection threshold for feat expression
`rank_score`	rank scores for both detection and expression to include
`min_feats`	minimum number of top feats to return
`min_genes`	deprecated, use min_feats
`verbose`	be verbose

Value#

data.table with marker feats

See Also#

findGiniMarkers