addCellMarkersToCGS: Add gene symbols and cell type marker information to cluster...

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

Add gene symbols and cell type marker information to cluster gene statistics

Description

Adds four new variables to the cluster-wise gene statistics dataframe of the scClustViz data object. Official gene symbols are added as variable genes. The remaining variables are used in plot_clusterGenes_markers to plot cell type marker genes. Variables cMu and cMs are logical vectors indicating genes that are unique to and shared across cell type markers respectively. Variable overCut indicates which genes should be labelled in the plot.

Usage

addCellMarkersToCGS(sCV, cellMarkersU, cellMarkersS, symbolMap)

Arguments

sCV	An object of class sCVdata.
cellMarkersU	Derived from the cellMarkers argument to runShiny. A list of the unique gene symbols for each cell type in cellMarkers.
cellMarkersS	Derived from the cellMarkers argument to runShiny. A list of the gene symbols common to two or more cell types in cellMarkers. Each entry is named for the indicies of cellMarkers that share the gene.
symbolMap	The output of map2symbol.

Value

The sCVdata object with the new variables added to ClustGeneStats.

See Also

findKeyType, map2symbol, and mapIds.

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.