Hello, I am conducting scATAC-seq analysis using the software ArchR. When executing addHarmony, an error occurs, indicating that the object 'HarmonyMatrix' cannot be found.

[wujian-njau]

#Use Harmony to remove batch effects
proj.filter <- addHarmony(ArchRProj = proj.filter,

• reducedDims = "IterativeLSI",
• name = "Harmony", #use Harmony to remove batch effects
• groupBy = "Sample", #because these are multiple samples, remove batch effects by sample
• force = T)
  Error in addHarmony(ArchRProj = proj.filter, reducedDims = "IterativeLSI", :
  object 'HarmonyMatrix' not found

[pati-ni]

Hi @wujian-njau , I suggest taking this issue to the ArchR repo. HarmonyMatrix has been dropped from Harmony2 algorithm and the proper interface is RunHarmony()