labelCellTypes | R Documentation |
A bare-bones method of predicting cell types from marker genes.
labelCellTypes(sCV, cellMarkers, symbolMap = NULL)
sCV |
An object of class |
cellMarkers |
The |
symbolMap |
Default=NULL. The output of |
Assigns cell type labels to each cluster based on the rank of median gene expression of marker genes for each cell type. There are many more intelligent methods for cell type prediction out there. See CellAssign, for example.
Returns the sCVdata object with an added attribute
'ClusterNames
' to Clusters(sCV)
containing the assigned cell
type names for each cluster. Stores the cellMarkers
list as an
attribute in Clusters(sCV)
. Also adds four new variables to
ClustGeneStats(sCV)
: Official gene symbols are added as variable
genes
. The remaining variables are used in
plot_clusterGenes_markers
to plot cell type marker genes in
the Shiny app (see runShiny
). 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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.