Find Marker Genes¶

findMarkers()

Identify marker genes for selected clusters.

findMarkers(
    gobject,
    expression_values = c("normalized", "scaled", "custom"),
    cluster_column = NULL,
    method = c("scran", "gini", "mast"),
    subset_clusters = NULL,
    group_1 = NULL,
    group_2 = NULL,
    min_expr_gini_score = 0.5,
     min_det_gini_score = 0.5,
    detection_threshold = 0,
    rank_score = 1,
    min_genes = 4,
    group_1_name = NULL,
    group_2_name = NULL,
    adjust_columns = NULL,
    ...
)

Arguments¶

gobject	giotto object
expression_values	gene expression values to use
cluster_column	clusters to use
method	method to use to detect differentially expressed genes
subset_clusters	selection of clusters to compare
group_1	group 1 cluster IDs from cluster_column for pairwise comparison
group_2	group 2 cluster IDs from cluster_column for pairwise comparison
min_expr_gini_score	gini: filter on minimum gini coefficient for expression
min_det_gini_score	gini: filter minimum gini coefficient for detection
detection_threshold	gini: detection threshold for gene expression
rank_score	gini: rank scores to include
min_genes	minimum number of top genes to return (for gini)
group_1_name	mast: custom name for group_1 clusters
group_2_name	mast: custom name for group_2 clusters
adjust_columns	mast: column in pDataDT to adjust for (e.g. detection rate)
…	additional parameters for the findMarkers function in scran or zlm function in MAST

Value¶

A data.table with marker genes

Details¶

Wrapper for all individual functions to detect marker genes for clusters.