findMastMarkers — findMastMarkers • Giotto

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

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

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

Value

data.table with marker genes

Details

This is a minimal convenience wrapper around the zlm from the MAST package to detect differentially expressed genes. Caution: with large datasets MAST might take a long time to run and finish

Examples


if (FALSE) {
data(mini_giotto_single_cell)

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