findGiniMarkers_one_vs_all

Source: R/differential_expression.R

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

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


data(mini_giotto_single_cell)

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

#> 
#>  start with cluster  1 
#> 
#>  start with cluster  2 
#> 
#>  start with cluster  3