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chuiqin / irGSEA

The integration of single cell rank-based gene set enrichment analysis
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irGSEA.integrate error #28

Open Lucyyang1991 opened 8 months ago

Lucyyang1991 commented 8 months ago

When I ran irGSEA.integrate, I got an error.

object = JoinLayers(object)
  object@assays$RNA$data = as(object = object@assays$RNA$data, Class = "dgCMatrix")
  object@assays$RNA$scale.data = as(object = object@assays$RNA$scale.data, Class = "matrix")
  object = irGSEA.score(object = object, species = "Mus musculus", assay = "RNA", slot = "data", category = "H", method = c("AUCell", "UCell", "singscore"))
  result.deg = irGSEA.integrate(object = object, group.by = resolution, method = c("AUCell", "UCell", "singscore"))

The error is listed below:

>   result.deg = irGSEA.integrate(object = object, group.by = resolution, method = c("AUCell", "UCell", "singscore"))
Error in irGSEA.integrate(object = object, group.by = resolution, method = c("AUCell",  : 
  Please imput correct `method`.
Lucyyang1991 commented 8 months ago

When I remove AUCell, things work. So I think is the problem of AUCell

 result.deg = irGSEA.integrate(object = object, group.by = resolution, method = c("UCell", "singscore"))
Calculate differential gene set : UCell
Calculate differential gene set : singscore
No sigficant genesets in cluster : 6, 7 after wilicox test
There were 16 warnings (use warnings() to see them)