`findMastMarkers_one_vs_all`¶

findMastMarkers_one_vs_all

Description¶

Identify marker genes for all clusters in a one vs all manner based on the MAST package.

Usage¶

findMastMarkers_one_vs_all(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  adjust_columns = NULL,
  pval = 0.001,
  logFC = 1,
  min_genes = 10,
  verbose = TRUE,
  ...
)

Arguments¶

Argument	Description
`gobject`	giotto object
`expression_values`	gene expression values to use
`cluster_column`	clusters to use
`subset_clusters`	selection of clusters to compare
`adjust_columns`	column in pDataDT to adjust for (e.g. detection rate)
`pval`	filter on minimal p-value
`logFC`	filter on logFC
`min_genes`	minimum genes to keep per cluster, overrides pval and logFC
`verbose`	be verbose
`...`	additional parameters for the zlm function in MAST

Value¶

data.table with marker genes

Seealso¶

``findMastMarkers` <#findmastmarkers>`_

Examples¶

data(mini_giotto_single_cell)

mast_markers = findMastMarkers_one_vs_all(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus')