Giter Club home page Giter Club logo

Comments (4)

jokergoo avatar jokergoo commented on July 17, 2024

What is your cola version? >= 2.0.0? Can you also provide the output from traceback()?

from cola.

msierk avatar msierk commented on July 17, 2024

Yes, cola 2.00. traceback and session info below. Thanks!

> functional_enrichment(rl) 
* enrich signature genes (k = 2) to BP terms for SD:skmeans on org.Hs.eg.db, 1/20
- 1163/6923 significant genes are taken from 2-group comparisons
 - on k-means group 1/2, 431 genes
Error in .local(object, ...) : 
  formal argument "prefix" matched by multiple actual arguments
In addition: Warning messages:
1: Quick-TRANSfer stage steps exceeded maximum (= 170850) 
2: Quick-TRANSfer stage steps exceeded maximum (= 150500) 
3: Quick-TRANSfer stage steps exceeded maximum (= 214050) 
4: Quick-TRANSfer stage steps exceeded maximum (= 182650) 
5: Quick-TRANSfer stage steps exceeded maximum (= 180050) 
6: Quick-TRANSfer stage steps exceeded maximum (= 204200) 
7: Quick-TRANSfer stage steps exceeded maximum (= 185150) 
8: Quick-TRANSfer stage steps exceeded maximum (= 183100) 

> traceback()
12: functional_enrichment(sig_gene[l], id_mapping = id_mapping, org_db = org_db, 
        ontology = ontology, min_set_size = min_set_size, max_set_size = max_set_size, 
        verbose = verbose, prefix = paste0(prefix, "  "), ...)
11: functional_enrichment(sig_gene[l], id_mapping = id_mapping, org_db = org_db, 
        ontology = ontology, min_set_size = min_set_size, max_set_size = max_set_size, 
        verbose = verbose, prefix = paste0(prefix, "  "), ...)
10: .local(object, ...)
9: functional_enrichment(object@list[[i]], gene_fdr_cutoff = gene_fdr_cutoff, 
       id_mapping = id_mapping, org_db = org_db, min_set_size = min_set_size, 
       max_set_size = max_set_size, prefix = "  ", ontology = ontology, 
       ...)
8: functional_enrichment(object@list[[i]], gene_fdr_cutoff = gene_fdr_cutoff, 
       id_mapping = id_mapping, org_db = org_db, min_set_size = min_set_size, 
       max_set_size = max_set_size, prefix = "  ", ontology = ontology, 
       ...)
7: .local(object, ...)
6: functional_enrichment(rl)
5: functional_enrichment(rl) at cola.R#49
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("~/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Krauze/Glioma_Andra_Krauze_Lab/cola.R", 
       echo = TRUE)`

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] tibble_3.1.7                  dplyr_1.0.9                   ssgsea.GBM.classification_1.0
 [4] devtools_2.4.3                usethis_2.1.6                 genefilter_1.76.0            
 [7] ComplexHeatmap_2.11.1         markdown_1.1                  knitr_1.39                   
[10] cola_2.0.0                    Biobase_2.54.0                BiocGenerics_0.40.0          

from cola.

jokergoo avatar jokergoo commented on July 17, 2024

Now it is fixed. Please update from GitHub.

from cola.

msierk avatar msierk commented on July 17, 2024

Thanks for the quick fix! And thanks for all the great packages you provide!

from cola.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.