carmonalab / genenmf Goto Github PK

Dear author
This is a great toolkit! However, when I library it in R, error occur.
The code is [
library(GeneNMF,lib.loc = "/share/home/User/miniconda3/envs/R4.3/lib/R/library")
Error: This is R 4.2.2, package ‘GeneNMF’ needs >= 4.3.0]
Is there a test of R version in your package (i gusses?), which make me can not library it

Hi,

I have two questions:

1. How to determine a reasonable number of MetaProgram (i.e., nprograms in function getMetaPrograms)?
2. How to cite your work?

Thanks

Hi
could you please explain what is the meaning of "Dropped 1 empty meta-programs"
after i run
geneNMF.metaprograms <- getMetaPrograms(geneNMF.programs,
nprograms=12,
max.genes=50,
hclust.method="ward.D2",
min.confidence=0.3)

Expecting a single value: [extent=0].

Hello, Thank you for providing such an excellent package.
In the GeneNMF demo, the code snippet:

geneNMF.programs <- multiNMF(seu.list, assay="SCT", slot="data", k=4:9, L1=c(0,0), do_centering=TRUE, nfeatures = 2000)

could you please explain why the parameter k was set to range from 4 to 9?
Thank you!