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csbl-usp / fcoex

The fcoex package implements an easy-to use interface to co-expression analysis based on the FCBF (Fast Correlation-Based Filter) algorithm. it was implemented especifically to deal with single-cell data. The modules found can be used to redefine cell populations, unrevel novel gene associations and predict gene function by guilt-by-association. The package structure is based on the CEMiTool package.
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mod_ora(fc, gmt_in) #3

Open mkorshe opened 4 years ago

mkorshe commented 4 years ago

I am trying to run:

fc <- mod_ora(fc, gmt_in)

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mod_ora’ for signature ‘"fcoex"’

It is the same for my and mini_pbmc dataset

mkorshe commented 4 years ago

Plus error is on the next step

save_plots(name = "fcoex_vignette_Seurat", fc, force = TRUE) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘save_plots’ for signature ‘"fcoex"’

lubianat commented 4 years ago

Hello @mkorshe, thank you for using fcoex. What version of R are you using? I`ll check it here.

mkorshe commented 4 years ago

Hello :)

I am using R version 4.0.2 (2020-06-22)

lubianat commented 4 years ago

@mkorshe I was not able to reproduce your errors here.

Is it possible that you loaded another package, which is masking the mod_ora function?

Can you try running fc <- fcoex::mod_ora(fc, gmt_in) and see if the error still happens? Thanks!

mkorshe commented 4 years ago

Well, I run this command:

fc <- fcoex::mod_ora(fc, gmt_in) Warning message: In fcoex::mod_ora(fc, gmt_in) : Enrichment is NULL. Either your gmt file is inadequate or your modules really aren't enriched for any of the pathways in the gmt file.

Bt in my session it looks like I have gmt files.

How can I solve it? And what can I use as another package for mimicking mod_ora function?

Thank you :)

lubianat commented 4 years ago

maybe modules really aren't enriched for any of the pathways in the gmt file? not really sure, sorry.

You can take the genes in each module and try https://maayanlab.cloud/Enrichr/