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')