The function markerGSEA calculates gene (marker) set enrichment of cluster-specific variable markers within bone cell type- or bone tissue-specific marker database.

Usage

markerGSEA(
  varMarkers,
  markers = NULL,
  systemLevel = "cellType",
  byDatabase = TRUE,
  minSize = 5,
  maxSize = 50000
)

Arguments

varMarkers: A data.frame containing variable markers for each cluster as reported by FindAllMarkers function from Seurat package.
markers: Optional user provided named list with markers.
systemLevel: Optional string specifying on which systematic level to perform enrichment, options: "cellType" or "tissue". Default: "cellType". Use only when NOT providing your own markers variable.
byDatabase: Optional logical variable specifying if enrichment should be performed separately for each database (i.e. source from which markers were obtained): option TRUE (default). Or if the database column in markerDatabase should be ignored and enrichment is done on all available markers for a given cellType or tissue: option FALSE. Use only when NOT providing your own markers variable.
minSize: Optional number specifying a minimal number of markers within a marker set to be considered (defaults to 5).
maxSize: Optional umber specifying a maximal number of markers within a marker set to be considered (defaults to 50000).

Value

data.frame with following variables: pathway (name of list variable with markers used for GSEA) / pval (p-value) / padj (adjusted p-value) / log2err (log2(error)) / ES (enrichment score) / NES (normalized enrichment score - useful for multiple comparisons) / size (number of overlaps) / leadingEdge (overlapping markers) / cluster (cluster number)

Examples

varMarkerFile = system.file("extdata", "cluster_variable_features.csv",
                            package = "BoneCellType")
varMarkers = read.csv(varMarkerFile)
GSEAres = markerGSEA(varMarkers)

# use own markers
markerList = cellType_list
GSEAresCustom = markerGSEA(varMarkers, markers=cellType_list)