getMarkerFeature(): Found less than 100 cells for background matching, Lowering k to 0

[Jiahuan90]

Hi rcorces,

I have encountered a problem: one of cell type number in ArchR project is 86 cells. When I ran getMarkerFeature() function to descover differential peaks among clusters, it met an error: "Found less than 100 cells for background matching, Lowering k to 0".

If the rare number cell type is of biological significance, how can I set parameters to overcome this problem?
Below is my code:

markersPeaks <- getMarkerFeatures(
                              ArchRProj = proj,
                              useMatrix = "PeakMatrix",
                              groupBy = "cell.type",
                              bias = c("TSSEnrichment", "log10(nFrags)"),
                              testMethod = "wilcoxon"

)

Thank you for your kindly help~~

[rcorces]

86 cells is simply not enough to make biologically meaningful conclusions from. There is really no way around that.

[Jiahuan90]

Thank you for your kindly help~