Differential peaks comparisons between combined groups

[yxiao832]

Hi ArchR team,

If I want to get the differential peaks between cluster1,2,3 (as one combined group) and cluster4,5,6 (as one combined background group )

should I use the following command:

markerTest <- getMarkerFeatures(
ArchRProj = proj,
useMatrix = "PeakMatrix",
groupBy = "Clusters",
testMethod = "wilcoxon",
bias = c("TSSEnrichment", "log10(nFrags)"),
useGroups = c("Cluster1","Cluster2","Cluster3"),
bgdGroups = c("Cluster4","Cluster5","Cluster6")
)

pma <- plotMarkers(seMarker = markerTest, name = c("Cluster1","Cluster2","Cluster3"), cutOff = "FDR <= 0.1 & abs(Log2FC) >= 1", plotAs = "MA")

Thank you very much!
Yang

[rcorces]

looks fine to me