findScranMarkers_one_vs_all: findScranMarkers_one_vs_all

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

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

findScranMarkers

Examples

data(mini_giotto_single_cell)

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

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.