Identify Marker Genes Using MAST

findMastMarkers()

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

A 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)
}