`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>`_