findMastMarkers#
Last Updated: Oct 02, 2023
Description#
Identify marker feats for selected clusters based on the MAST package.
Usage#
findMastMarkers(
gobject,
feat_type = NULL,
spat_unit = NULL,
expression_values = c("normalized", "scaled", "custom"),
cluster_column,
group_1 = NULL,
group_1_name = NULL,
group_2 = NULL,
group_2_name = NULL,
adjust_columns = NULL,
verbose = FALSE,
...
)
Arguments#
|
giotto object |
|
feature type |
|
spatial unit |
|
feat expression values to use |
|
clusters to use |
|
group 1 cluster IDs from cluster_column for pairwise comparison |
|
custom name for group_1 clusters |
|
group 2 cluster IDs from cluster_column for pairwise comparison |
|
custom name for group_2 clusters |
|
column in pDataDT to adjust for (e.g. detection rate) |
|
be verbose |
|
additional parameters for the zlm function in MAST |
Details#
This is a minimal convenience wrapper around the zlm
from the MAST
package to detect differentially expressed feats. Caution: with large
datasets MAST might take a long time to run and finish
Value#
data.table with marker feats