Hi,

I have 3 clusters of cell and I want to find marker genes specific to each cluster; By markersAUCPR function in URD package I am doing so

> markersAUCPR(object, clust.1 = "1", clust.2 = NULL, cells.1 = NULL,
+              cells.2 = NULL, clustering = "Louvain-60", effect.size = 2,
+              frac.must.express = 0.2, frac.min.diff = 0.2, genes.use = NULL)

I think clust.1 = "1" vs clust.2 = NULL means compare cells in cluster one vs all cells in two other clusters and return marker genes specific to cluster 1; By doing so I am getting 9000 marker genes while I only have 11000 genes in my genome. Additionally, when I am plotting the expression of marker genes defined for cluster 1 on URD cluster, I expect only these genes become yellow in cells in cluster 1 but all heat map become yellow (please look at picture). So I suspect if my interpretation of this function for finding marker genes specific to each cluster is right. I read the source code but nothing new I got from that.

Could somebody have a look at this function and tell me if I am wrong?

Thanksa lot