findMarkers#
Last Updated: Jan 14, 2025
Description#
Identify marker feats for selected clusters.
Usage#
findMarkers(
gobject,
spat_unit = NULL,
feat_type = NULL,
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_feats = 4,
min_genes = NULL,
group_1_name = NULL,
group_2_name = NULL,
adjust_columns = NULL,
...
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
feat expression values to use |
|
clusters to use |
|
method to use to detect differentially expressed feats |
|
selection of clusters to compare |
|
group 1 cluster IDs from cluster_column for pairwise comparison |
|
group 2 cluster IDs from cluster_column for pairwise comparison |
|
gini: filter on minimum gini coefficient for expression |
|
gini: filter minimum gini coefficient for detection |
|
gini: detection threshold for feat expression |
|
gini: rank scores to include |
|
minimum number of top feats to return (for gini) |
|
deprecated, use min_feats |
|
mast: custom name for group_1 clusters |
|
mast: custom name for group_2 clusters |
|
mast: column in pDataDT to adjust for (e.g. detection rate) |
|
additional parameters for the findMarkers function in scran or zlm function in MAST |
Details#
Wrapper for all individual functions to detect marker feats for clusters.
Value#
data.table with marker feats
See Also#
findScranMarkers
, findGiniMarkers
and findMastMarkers