findMastMarkers: findMastMarkers

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

findMastMarkers

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.