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
)
giotto object
gene expression values to use
clusters to use
selection of clusters to compare
filter on minimum gini coefficient on expression
filter on minimum gini coefficient on detection
detection threshold for gene expression
rank scores for both detection and expression to include
minimum number of top genes to return
be verbose
data.table with marker genes
data(mini_giotto_single_cell)
gini_markers = findGiniMarkers_one_vs_all(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus')