SingleR fails with Seurat 3.0.0 installed: no slot of name "data" for this object of class "Seurat"

[plijnzaad]

When trying to run Singler 0.2.2 with Seurat 3.0.0, I get the following error:

singler = CreateSinglerSeuratObject(counts=input2,
  annot = NULL,
  project.name="hihi",
  min.genes = 500,
  technology = "CEL-Seq2",
  species = "Human",
  citation = "unk",
  ref.list = list(), 
  normalize.gene.length = FALSE,  
  variable.genes = "de",
  fine.tune = FALSE,
  reduce.file.size = FALSE,
  do.signatures = FALSE,
  min.cells = 2, 
  npca = 10,
  do.main.types = TRUE)

I get

Error in CreateSinglerSeuratObject(counts = input2, annot = NULL, project.name = "hihi",  :
  no slot of name "data" for this object of class "Seurat"

It works fine when I'm using Seurat 2.4.3. It looks like the new SingleR code still has some remnants of the Seurat 2 API, which is unfortunate. This is using

R.version$version.string [1] "R version 3.5.1 (2018-07-02)"
package.version("SingleR")   [1] "0.2.2"
packageVersion("Seurat") [1] '3.0.0'

[dviraran]

Try reinstalling SingleR. I fixed this issue yesterday.

[plijnzaad]

Brilliant, seems to work, thanks.

I noticed that the version is still

> packageVersion("SingleR")
[1] '0.2.2'

Maybe you want to bump this to make it easier to see if the right version is installed.

Cheers,

Philip

[dviraran]

You are right... I need to update the version... its probably time that I call it 1.0.0....