Error about GenerateGenesets

[simaxiaoyao]

gs <- GenerateGenesets(SSc) Reading gmt file... Error in x[1] : object of type 'S4' is not subsettable or gs <- GenerateGenesets(PSc) Reading gmt file... Error in x[1] : object of type 'S4' is not subsettable

I just rum the code with the tutorial, but when I run 'gs <- GenerateGenesets(SSc)' or 'gs <- GenerateGenesets(PSc)', some errors happens. Could you tell me how solve this error?

[CrazyOrange233]

I had the same problem when I was using the R package, did you solve it?

[mj-jimenez]

Hi everybody,

Sorry, we haven't updated the vignette yet. We have introduced a new function to charge pre-loaded collections. Please run

GetCollection(SSc, n.genes = 250, mode = c("up", "down"))

Note that the parameter comparison is not valid anymore as Beyondcell handles it internally.

Alternatively, if you have a custom GMT please run

GenerateGenesets(path_to_geneset)

[SGMartin]

Solved!

[YongguangWei]

Using the above method, it still appeared “Error in x[1] : object of type 'S4' is not subsettable”. How can we solve it

[SGMartin]

Hi @YongguangWei

To address your issue we need a couple of details:

1. Which beyondcell version you are using at the moment.
2. A minimal code snippet that triggers the error, so that we may attempt to reproduce it.

Yours

[YongguangWei]

1. The version of r package "beyondcell" was 2.2.1 version.
2. Code: >GetCollection(SSc, n.genes = 250, mode = c("up", "down"))

   gs <- GenerateGenesets(PSc) Reading gmt file... Error in x[1] : object of type 'S4' is not subsettable

[SGMartin]

It seems from your code that you are trying to load the PSc collection using GenerateGenesets instead of GetCollection.

PSc and SSc are predefined collections and thus, you can load both of them the same way using GetCollection. GenerateGenesets is now reserved for loading genesets from a gmt file.

[YongguangWei]

¡Muchas gracias!

[SGMartin]

Marked as solved