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rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
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pseudotime.tree #17

Closed Yale73 closed 4 years ago

Yale73 commented 4 years ago

Hi, Rezakj, Thanks for this powerful l tool. I ran an issue to run the pseudotime.tree. The error is 

Error in `[.data.frame`(x, r, vars, drop = drop) : 
  undefined columns selected

MyGenes are correct

> MyGenes[1:5]
[1] "Cd209a" "Cd209d" "Il4i1"  "H2.Oa"  "Ccr7"

But when I run the colnames ()

> colnames(my.obj)
NULL

Whether it means there are no columns, therefore, I can not run the function? But I have got the marker.genes and MyGenes.

Thanks for your help, Yale

rezakj commented 4 years ago

Hi Yale,

Thank you for using iCellR,

And yes my bad, I didn't mention that you need to also run this:

my.obj <- clust.avg.exp(my.obj)

Then run it and it should work. 

pseudotime.tree(my.obj,
   marker.genes = MyGenes,
   type = "unrooted",
   clust.method = "complete")

Reza

Yale73 commented 4 years ago

Hi Reza,

Thanks so much. It works great. I forgot I merged the Seurat and the iCellR, and skipped some steps.

Thanks again, Yale