Find Marker Genes Using Gini in One vs. All Manner¶

findGiniMarkers_one_vs_all()

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¶

A data.table with marker genes

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