Identify marker genes for all clusters in a one vs all manner based on scran's implementation of findMarkers.

findScranMarkers_one_vs_all(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  pval = 0.01,
  logFC = 0.5,
  min_genes = 10,
  verbose = TRUE,
  ...
)

Arguments

gobject

giotto object

expression_values

gene expression values to use

cluster_column

clusters to use

subset_clusters

subset of clusters to use

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 findMarkers function in scran

Value

data.table with marker genes

See also

Examples


data(mini_giotto_single_cell)

scran_markers = findScranMarkers_one_vs_all(gobject = mini_giotto_single_cell,
                                            cluster_column = 'leiden_clus')