decoupleR::get_collectri() returns always human regulons

[riederd]

decoupleR::get_collectri() returns always human regulons, no matter what organism is specified:

> xx <- decoupleR::get_collectri(organism=10090, split_complexes=FALSE)
[2023-10-23 13:11:57] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.
> yy <- decoupleR::get_collectri(organism=9606L, split_complexes=FALSE)
[2023-10-23 13:22:06] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.
> zz <- decoupleR::get_collectri(organism='noorganism', split_complexes=FALSE)
[2023-10-23 13:33:56] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.
> all.equal(xx,yy)
[1] TRUE
> all.equal(xx,zz)
[1] TRUE

I'd expect that if organism=10090 or organism='mouse' is specified, regulons with mouse gene symbols will be returned and if an invalid organism organism='noorganism' is specified an error will be thrown.

Is there anything I'm doing wrong?

[riederd]

BTW I'm using the following versions:

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/local/bioinf/R/R-4.2.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] clusterProfiler_4.6.2 OmnipathR_3.9.8       devtools_2.4.5        usethis_2.2.2        
 [5] org.Mm.eg.db_3.16.0   AnnotationDbi_1.60.2  IRanges_2.32.0        S4Vectors_0.36.2     
 [9] Biobase_2.58.0        BiocGenerics_0.44.0   ComplexHeatmap_2.14.0 decoupleR_2.6.0      
[13] stringr_1.5.0         tibble_3.2.1          tidyr_1.3.0           dplyr_1.1.3          
[17] readr_2.1.4           ggrepel_0.9.3         ggplot2_3.4.2         edgeR_3.40.2         
[21] limma_3.54.2          docopt_0.7.1          conflicted_1.2.0 

[PauBadiaM]

Hi @riederd,

Could you restart your session and try again? Else see here: https://github.com/saezlab/decoupleR/issues/87#issuecomment-1605315864 I would also try to install the latest decoupleR and Omnipath version from GitHub:

remotes::install_github('saezlab/omnipathr')
remotes::install_github('saezlab/decoupleR')

Let me know how it goes, hope this is helpful!

[riederd]

Hi @PauBadiaM ,

thanks for your hint. Restarting the R session does not help, however installing the development version of decoupleR did the trick. (For Omnipath, I already had installed the dev version)