findGiniMarkers_one_vs_all#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/differential_expression.R#L527

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#

Argument

Description

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

Seealso#

`findGiniMarkers <#findginimarkers>`__