Get Marker Feature accross Time

[adrdufour]

Hello,

I would like to compare the chromatin accessibility in a cluster in this evolution through time.
To do so i create a new cell annotation like this :

archrproj <- addCellColData(
ArchRProj = archrproj,
data = paste0(getCellColData(archrproj)$Clusters, "_", getCellColData(archrproj)$Time),
name = "Cluster_Time",
cells = getCellNames(archrproj),
force = FALSE
)

and then following archr tutorials i perform differential analysis between stage like this :

markerTest <- getMarkerFeatures(
ArchRProj = archrproj,
useMatrix = "PeakMatrix",
groupBy = "Cluster_Time",
testMethod = "wilcoxon",
bias = c("TSSEnrichment", "log10(nFrags)"),
useGroups = "C2_J7",
bgdGroups = "C2_J11"
)

pma <- plotMarkers(seMarker = markerTest, name = "C2_J7", cutOff = "FDR <= 0.1 & abs(Log2FC) >= 1", plotAs = "MA")
pma

Which produce this figure :

But i notice that if reverse the group, the resulting volcanoplot is different

markerTest <- getMarkerFeatures(
ArchRProj = archrproj,
useMatrix = "PeakMatrix",
groupBy = "Cluster_Time",
testMethod = "wilcoxon",
bias = c("TSSEnrichment", "log10(nFrags)"),
useGroups = "C2_J11",
bgdGroups = "C2_J7"
)

pma <- plotMarkers(seMarker = markerTest, name = "C2_J11", cutOff = "FDR <= 0.1 & abs(Log2FC) >= 1", plotAs = "MA")
pma

Thank you for you helps.
Adrien Dufour.