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, ... )
| 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 |
data.table with marker genes
Wrapper for all individual functions to detect marker genes for clusters.