`findGiniMarkers_one_vs_all`¶

findGiniMarkers_one_vs_all

Description¶

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

Usage¶

findGiniMarkers_one_vs_all(
  gobject,
  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_genes = 4,
  verbose = TRUE
)

Arguments¶

Argument	Description
`gobject`	giotto object
`expression_values`	gene 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 gene expression
`rank_score`	rank scores for both detection and expression to include
`min_genes`	minimum number of top genes to return
`verbose`	be verbose

Value¶

data.table with marker genes

Seealso¶

``findGiniMarkers` <#findginimarkers>`_

Examples¶

data(mini_giotto_single_cell)

gini_markers = findGiniMarkers_one_vs_all(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus')