findMastMarkers_one_vs_all#
Last Updated: Jan 14, 2025
Description#
Identify marker feats for all clusters in a one vs all manner based on the MAST package.
Usage#
findMastMarkers_one_vs_all(
gobject,
feat_type = NULL,
spat_unit = NULL,
expression_values = c("normalized", "scaled", "custom"),
cluster_column,
subset_clusters = NULL,
adjust_columns = NULL,
pval = 0.001,
logFC = 1,
min_feats = 10,
min_genes = NULL,
verbose = TRUE,
...
)
Arguments#
|
giotto object |
|
feature type |
|
spatial unit |
|
feat expression values to use |
|
clusters to use |
|
selection of clusters to compare |
|
column in pDataDT to adjust for (e.g. detection rate) |
|
filter on minimal p-value |
|
filter on logFC |
|
minimum feats to keep per cluster, overrides pval and logFC |
|
deprecated, use min_feats |
|
be verbose |
|
additional parameters for the zlm function in MAST |
Value#
data.table with marker feats
See Also#
findMastMarkers