findScranMarkers_one_vs_all

findScranMarkers_one_vs_all

Description

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

Usage

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

Argument	Description
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

Seealso

``findScranMarkers` <#findscranmarkers>`_

Examples

data(mini_giotto_single_cell)

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