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farrellja / URD

URD - Reconstruction of Branching Developmental Trajectories
GNU General Public License v3.0
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object@group instead of object@group.ids? #4

Closed Kgies10 closed 6 years ago

Kgies10 commented 6 years ago

Hi there,

I'm trying to do gene cascade in a 2D URD tree, but when I call aucprTestAlongTree as in: 

markers <- aucprTestAlongTree(objTree, pseudotime="pseudotime", tips=tip,
              log.effect.size=0.4, auc.factor = 1.25, max.auc.threshold = 0.85, 
              frac.must.express = 0.1, frac.min.diff = 0, genes.use=genes.use, 
              only.return.global=F, must.beat.sibs=0.6, report.debug=T)

I get this error: 

Error in markersAUCPR(object = object, cells.1 = cells.1, cells.2 = cells.2,  : 
  no slot of name "group" for this object of class "URD"

So I looked at markersAUCPR and it calls: 

if (is.null(clustering)) {
    clust.use <- object@group

But I didn't think URD objects had a slot called "group" just "group.ids". Why does markersAUCPR reference object@group?

For reference my tree, objTree, is an URD object: 18385 genes x 23602 cells. Any help would be greatly appreciated! Many thanks!

farrellja commented 6 years ago

Just before releasing the software, I removed some deprecated slots from the URD object, which included @group. I thought I had removed all references to it, but clearly missed a couple. I just fixed the bug, and increased the version number to 1.0.1. So, go ahead and update your URD installation (devtools::install_github(repo="farrellja/URD")) and it should be corrected.

Kgies10 commented 6 years ago

Great, thanks for updating!