findMastMarkers#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/differential_expression.R#L650

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#

Argument

Description

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 <#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