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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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In file(con, "wb") : cannot open file #99

Closed DLGisch closed 3 years ago

DLGisch commented 3 years ago

Describe the bug The bug happens with pin_name_path 'String' gene_sets 'Reactome' and 'GO-BP', but not happens with pin_name_path 'String' gene_sets 'KEGG'. The directory 'term_visualizations' is empty and there aren't .html files and not created output_df too.

To Reproduce

Steps to reproduce the behavior: output_df <- run_pathfindR(data, output_dir = STRING_GOBP/), gene_sets = 'GO-BP', min_gset_size = 1, max_gset_size = 500, p_val_threshold=0.05, pin_name_path = 'STRING', plot_enrichment_chart=FALSE, n_processes = 2 )

Testing input

The input looks OK

Processing input. Converting gene symbols,

      if necessary (and if human gene symbols provided)

Number of genes provided in input: 1472 Number of genes in input after p-value filtering: 1472 pathfindR cannot handle p values < 1e-13. These were changed to 1e-13 Could not find any interactions for 134 (9.1%) genes in the PIN Final number of genes in input: 1337

Performing Active Subnetwork Search and Enrichment

Processing the enrichment results over all iterations

Annotating involved genes and visualizing enriched terms

Error in file(con, "wb") : cannot open the connectionxogenous peptide antigen via MHC class I, TAP-dependent
In addition: Warning message: In file(con, "wb") : cannot open file 'term_visualizations/antigen_processing_and_presentation_of_exogenous_peptide_antigen_via_MHC_class_I,_TAP-dependent.png': No such file or directory

Desktop (please complete the following information):

R Session Information: R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041) PathfindR 1.6.1 Additional context Java version 8 Update 261

Can you give some idea about issue? Thanks in advance!

egeulgen commented 3 years ago

hey @DLGisch,

Some users encountered a similar issue before and it is fixed in the current version (1.6.2). The binary is not available yet but you can install the latest version via devtools:

install.packages("devtools") # if you have not installed "devtools" 
devtools::install_github("egeulgen/pathfindR")

Let me know if updating resolves the issue, Best, -E

DLGisch commented 3 years ago

Update fix the problem! Thank you for help me.