findMarkers_one_vs_all: findMarkers_one_vs_all

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

findMarkers_one_vs_all

Description

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

Usage

findMarkers_one_vs_all(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  method = c("scran", "gini", "mast"),
  pval = 0.01,
  logFC = 0.5,
  min_feats = 10,
  min_genes = NULL,
  min_expr_gini_score = 0.5,
  min_det_gini_score = 0.5,
  detection_threshold = 0,
  rank_score = 1,
  adjust_columns = NULL,
  verbose = TRUE,
  ...
)

Arguments

gobject	giotto object
feat_type	feature type
spat_unit	spatial unit
expression_values	feat expression values to use
cluster_column	clusters to use
subset_clusters	selection of clusters to compare
method	method to use to detect differentially expressed feats
pval	scran & mast: filter on minimal p-value
logFC	scan & mast: filter on logFC
min_feats	minimum feats to keep per cluster, overrides pval and logFC
min_genes	deprecated, use min_feats
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 feat 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 feats for clusters.

Value

data.table with marker feats

See Also

findScranMarkers_one_vs_all, findGiniMarkers_one_vs_all and findMastMarkers_one_vs_all

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.