findMarkers#

Last Updated: Sep 07, 2023

Description#

Identify marker feats for selected clusters.

Usage#

findMarkers(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column = NULL,
  method = c("scran", "gini", "mast"),
  subset_clusters = NULL,
  group_1 = NULL,
  group_2 = 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,
  group_1_name = NULL,
  group_2_name = NULL,
  adjust_columns = NULL,
  ...
)

Arguments#

`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`expression_values`	feat expression values to use
`cluster_column`	clusters to use
`method`	method to use to detect differentially expressed feats
`subset_clusters`	selection of clusters to compare
`group_1`	group 1 cluster IDs from cluster_column for pairwise comparison
`group_2`	group 2 cluster IDs from cluster_column for pairwise comparison
`min_expr_gini_score`	gini: filter on minimum gini coefficient for expression
`min_det_gini_score`	gini: filter minimum gini coefficient for detection
`detection_threshold`	gini: detection threshold for feat expression
`rank_score`	gini: rank scores to include
`min_feats`	minimum number of top feats to return (for gini)
`min_genes`	deprecated, use min_feats
`group_1_name`	mast: custom name for group_1 clusters
`group_2_name`	mast: custom name for group_2 clusters
`adjust_columns`	mast: column in pDataDT to adjust for (e.g. detection rate)
`...`	additional parameters for the findMarkers function in scran or zlm function in MAST

Details#

Wrapper for all individual functions to detect marker feats for clusters.

Value#

data.table with marker feats

See Also#

findScranMarkers, findGiniMarkers and findMastMarkers