findGiniMarkers_one_vs_all: findGiniMarkers_one_vs_all

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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

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

See Also

findGiniMarkers

Examples

    findGiniMarkers_one_vs_all(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.