Error when calculating GSVA based on UCell method

[YuxinYin0906]

Hi,

Thank you for making this amazing package! It has been a life saver for me.
However, I ran into a problem when trying to calculate gsva results using the method "UCell".
` #annotation
hsko<-buildAnnot(species="mouse",keytype="SYMBOL",anntype="GO")

#result based on ssgsea
res<-scgsva(scRNA_all_int,hsko,method="UCell") ## or use UCell`

The error message is as followed:

"Error in calculate_Uscore(m, features = features, maxRank = maxRank, chunk.size = chunk.size, :
One or more signatures contain more genes than maxRank parameter.
Increase maxRank parameter or make shorter signatures
Calls: scgsva".

I tried to change the anntype to "KEGG" and the function works smoothly, so I guess it's due to the fact that GO is a more enriched dataset than KEGG.
I understand that this might be more related to the UCell package, but I wonder if there's any way we could set the parameter for maxrank in the scgsva() function.

[guokai8]

Hi @YuxinYin0906,
I will take a look at it and try to fix it soon. I guess you are right.
K

[merckey]

I think you can add one additional parameter from UCell maxRank.

res<-scgsva(scRNA_all_int,hsko,method="UCell", maxRank = 3000)

[guokai8]

@merckey
Yes. I will add this, and you can directly add the "maxRank" when you run it now.
Thanks!
K