Known cell markers

Objects must contain Ensembl gene identifiers in the geneId column. We must avoid any matching operations based on the gene names, since these change often and can mismatch easily.

Usage

KnownMarkers(markers, known, ...)

# S4 method for SeuratMarkersPerCluster,CellTypeMarkers
KnownMarkers(markers, known, promiscuousThreshold = 0L)

Arguments

markers

SeuratMarkers or SeuratMarkersPerCluster.

known

CellTypeMarkers. Grouped by cellType column. Known markers data.frame imported by readCellTypeMarkers or pulled from internal cell cycle markers data.

promiscuousThreshold

integer(1). Minimum number of clusters required to consider a gene marker promiscuous. Set to 0 to disable promiscuous marker filtering.

...

Additional arguments.

Value

KnownMarkers.

Note

Updated 2022-06-09.

Examples

data(cellTypeMarkersList, package = "AcidSingleCell")
data(SeuratMarkersPerCluster, package = "AcidTest")

## SeuratMarkersPerCluster ====
markers <- SeuratMarkersPerCluster
known <- cellTypeMarkersList[["homoSapiens"]]
x <- KnownMarkers(markers = markers, known = known)
summary(x)
#> [1] "KnownMarkers object of length 10 with 0 metadata columns"