get_collectri is not able to fetch the right organism

[tamerbio]

Dear @PauBadiaM , I tried to apply get_collectri on mouse bulk RNA-seq data however the function returned a human gene regulatory network ids. which probably shows an error message in the downstream analysis and visualization. could you please double-check this function on mouse gene IDs? moreover, you mentioned in the vignette that the rat database is also available but I was not able to find it. thank you so much

best, Tamer

[PauBadiaM]

Hi @tamerbio,

Could you install the latest version from GitHUb and try again:

remotes::install_github('saezlab/decoupleR')

Let me know how it goes!

[tamerbio]

Hi @PauBadiaM, thanks for your quick reply. I tried already but still the same error. net <- get_collectri (organism = "mouse", split_complexes=FALSE)

[2024-02-22 09:42:49] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.
> net
# A tibble: 42,595 × 3
   source target   mor
   <chr>  <chr>  <dbl>
 1 MYC    TERT       1
 2 SPI1   BGLAP      1
 3 SMAD3  JUN        1
 4 SMAD4  JUN        1

contrast_acts <- run_wmean(mat= deg[, 'stat', drop=FALSE], net=net,
                           .source='source', .target='target',
                           .mor='mor', times = 100, minsize = 5)

Error in filt_minsize(rownames(mat), network, minsize) : 
  Network is empty after intersecting it with mat and
filtering it by sources with at least 5 targets. Make sure mat and 
network have shared target features or reduce the number assigned to minsize

thanks much Tamer

[PauBadiaM]

Hi @tamerbio ,

Mhm strange, have you restarted your R session? This should work with the GitHub version:

net <- get_collectri (organism = "mouse", split_complexes=FALSE)
net

# A tibble: 38,665 × 3
   source target   mor
   <chr>  <chr>  <dbl>
 1 Myc    Tert       1
 2 Spi1   Bglap2     1
 3 Spi1   Bglap      1
 4 Spi1   Bglap3     1

Can you print which decoupleR and OmnipathR version you have?

[tamerbio]

Thanks much @PauBadiaM, it did work

thanks a lot Tamer

[tamerbio]

I wish you could include rat data for PROGENy function. thanks again Tamer

[PauBadiaM]

Hi @tamerbio,

You can retrieve it easily:

net <- get_collectri(organism = "rat")
net

# A tibble: 24,372 × 3
   source target   mor
   <chr>  <chr>  <dbl>
 1 Myc    Tert       1
 2 Spi1   Bglap      1
 3 Smad3  Jun        1
 4 Smad4  Jun        1