findMarkers_one_vs_all

findMarkers_one_vs_all

Description

Identify marker genes for all clusters in a one vs all manner.

Usage

findMarkers_one_vs_all(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  method = c("scran", "gini", "mast"),
  pval = 0.01,
  logFC = 0.5,
  min_genes = 10,
  min_expr_gini_score = 0.5,
  min_det_gini_score = 0.5,
  detection_threshold = 0,
  rank_score = 1,
  adjust_columns = NULL,
  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
method	method to use to detect differentially expressed genes
pval	scran & mast: filter on minimal p-value
logFC	scan & mast: filter on logFC
min_genes	minimum genes to keep per cluster, overrides pval and logFC
min_expr_gini_score	gini: filter on minimum gini coefficient for expression
min_det_gini_score	gini: filter minimum gini coefficient for detection
detection_threshold	gini: detection threshold for gene expression
rank_score	gini: rank scores to include
adjust_columns	mast: column in pDataDT to adjust for (e.g. detection rate)
verbose	be verbose
...	additional parameters for the findMarkers function in scran or zlm function in MAST

Details

Wrapper for all one vs all functions to detect marker genes for clusters.

Value

data.table with marker genes

Seealso

``findScranMarkers_one_vs_all` <#findscranmarkersonevsall>`_ , ``findGiniMarkers_one_vs_all` <#findginimarkersonevsall>`_ and ``findMastMarkers_one_vs_all` <#findmastmarkersonevsall>`_