KnownMarkers: Known cell markers

In acidgenomics/pointillism: Single-cell RNA-seq toolkit

Known cell markers

Description

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 signature '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)

acidgenomics/pointillism documentation built on Oct. 18, 2023, 4:11 p.m.