Comments (4)
What is your cola version? >= 2.0.0? Can you also provide the output from traceback()
?
from cola.
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.
Now it is fixed. Please update from GitHub.
from cola.
Thanks for the quick fix! And thanks for all the great packages you provide!
from cola.
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from cola.