Identify marker genes for all clusters in a one vs all manner.
findMarkers_one_vs_all( gobject, expression_values = c("normalized", "scaled", "custom"), cluster_column, subset_clusters = NULL, method = c("scran", "gini", "mast"), pval = 0.01, logFC = 0.5, min_genes = 10, min_expr_gini_score = 0.5, min_det_gini_score = 0.5, detection_threshold = 0, rank_score = 1, adjust_columns = NULL, verbose = TRUE, ... )
| gobject | giotto object |
|---|---|
| expression_values | gene expression values to use |
| cluster_column | clusters to use |
| subset_clusters | selection of clusters to compare |
| method | method to use to detect differentially expressed genes |
| pval | scran & mast: filter on minimal p-value |
| logFC | scan & mast: filter on logFC |
| min_genes | minimum genes to keep per cluster, overrides pval and logFC |
| 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 |
| adjust_columns | mast: column in pDataDT to adjust for (e.g. detection rate) |
| verbose | be verbose |
| ... | additional parameters for the findMarkers function in scran or zlm function in MAST |
data.table with marker genes
Wrapper for all one vs all functions to detect marker genes for clusters.