findMarkers: findMarkers

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

findMarkers

Description

Identify marker genes for selected clusters.

Usage

findMarkers(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column = NULL,
  method = c("scran", "gini", "mast"),
  subset_clusters = NULL,
  group_1 = NULL,
  group_2 = NULL,
  min_expr_gini_score = 0.5,
  min_det_gini_score = 0.5,
  detection_threshold = 0,
  rank_score = 1,
  min_genes = 4,
  group_1_name = NULL,
  group_2_name = NULL,
  adjust_columns = NULL,
  ...
)

Arguments

gobject	giotto object
expression_values	gene expression values to use
cluster_column	clusters to use
method	method to use to detect differentially expressed genes
subset_clusters	selection of clusters to compare
group_1	group 1 cluster IDs from cluster_column for pairwise comparison
group_2	group 2 cluster IDs from cluster_column for pairwise comparison
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
min_genes	minimum number of top genes to return (for gini)
group_1_name	mast: custom name for group_1 clusters
group_2_name	mast: custom name for group_2 clusters
adjust_columns	mast: column in pDataDT to adjust for (e.g. detection rate)
...	additional parameters for the findMarkers function in scran or zlm function in MAST

Details

Wrapper for all individual functions to detect marker genes for clusters.

Value

data.table with marker genes

See Also

findScranMarkers, findGiniMarkers and findMastMarkers

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