Error: 'SubsetData' is not an exported object from 'namespace:Seurat'

[ScienceBear]

Hi Christian,

First of all, great package. Hope developing it goes well!

I am trying to run scWGNA.compare.report and get the following error:

Quitting from lines 47-73 (scWGCNA.comparative_report.Rmd) Error: 'SubsetData' is not an exported object from 'namespace:Seurat'

I have played around with scWGCNA.comparative_report.Rmd and changed the function

for (i in 1:length(my.test)) { my.test[[i]] = Seurat::SubsetData(my.test[[i]], features = my.ortho[,my.ortho.sp[i]]) }

at the Seurat::SubsetData to most iterations of that function I can think of, but I get the same error. Do you have any advice?

Best wishes,

Luke Dabin

[ScienceBear]

I have managed to get past this by changing lines 61-63 to

for (i in 1:length(my.test)) { my.test[[i]] = subset(my.test[[i]], features = my.ortho[,my.ortho.sp[i]]) }

There was an issue with the values I was using in data and test (I was literally using a list of seurat objects in my workspace for test) and changing both values to the same object fixed this.

I am now stuck on

_ortho
Data frame. As many columns as species used only listing 1-to-1 orthologous genes. The species of the reference MUST always be column no. 1

ortho.sp
Vector numeric. Indicating to which species in ortho each test sample belongs to._

Could you perhaps provide an example of what these should look like? With ortho I only have one species, but ortho.sp should be numeric, so putting Mm in column 1 of ortho doesn't seem sensible. I tried populating column 1 of ortho with the numeric 1, and having my ortho sp c(1,1,1,1) gives me the following message:

_Quitting from lines 47-73 (scWGCNA.comparativereport.Rmd) Error: Cannot find '1' in this Seurat object

[CFeregrino]

Hello! Apologies for not answering in forever. I was caught in moving jobs, moving countries, labs, projects, etc. Thank you for your interest and your messages, the original version had a couple of issues. I have made a big update in the package, and provided a workflow in the homepage, in case you still want to give it a try. It now works as intended, as a package and not just running a very long RMD script. Thanks!