`findMarkers`¶

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¶

Argument	Description
`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

Seealso¶

``findScranMarkers` <#findscranmarkers>`_ , ``findGiniMarkers` <#findginimarkers>`_ and ``findMastMarkers` <#findmastmarkers>`_