findMastMarkers_one_vs_all

Source: R/differential_expression.R

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

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

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

See also

findMastMarkers

Examples


data(mini_giotto_single_cell)

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