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#

`gobject`	giotto object
`feat_type`	feature type
`spat_unit`	spatial unit
`expression_values`	feat expression values to use
`cluster_column`	clusters to use
`group_1`	group 1 cluster IDs from cluster_column for pairwise comparison
`group_1_name`	custom name for group_1 clusters
`group_2`	group 2 cluster IDs from cluster_column for pairwise comparison
`group_2_name`	custom name for group_2 clusters
`adjust_columns`	column in pDataDT to adjust for (e.g. detection rate)
`verbose`	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