findMastMarkers

findMastMarkers

Description

Identify marker genes for selected clusters based on the MAST package.

Usage

findMastMarkers(
  gobject,
  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

expression_values

gene 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 genes. Caution: with large datasets MAST might take a long time to run and finish

Value

data.table with marker genes

Examples

data(mini_giotto_single_cell)

mast_markers = findMastMarkers(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus',
group_1 = 1,
group_2 = 2)