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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Connection issue with pathfindR #17

Closed engelsdaniel closed 5 years ago

engelsdaniel commented 5 years ago

Hi,

when running run_pathfindR(df) I get the warning message: Cannot connect to server. I have disabled the firewall, etc., did not work out.

Best, D

egeulgen commented 5 years ago

Hello, This may be due to an issue in one of the dependencies of pathfindR or an issue with R itself. Would you mind sharing the entire run's screen output? Best, -E

engelsdaniel commented 5 years ago

Sure!

names(data_pathway) <- c("Gene.symbol", "logFC", "adj.P.Val") data_pathway <- subset(data_pathway, data_pathway$adj.P.Val > 0) output <- run_pathfindR(data_pathway[1:10, ])

Testing input

The input looks OK

Processing input. Converting gene symbols, if necessary (and if human gene symbols provied)

Could not find any interactions for 1 (50%) genes in the PIN

Performing Active Subnetwork Search and Enrichment

Error in { : task 1 failed - "kann Verbindung nicht öffnen" In addition: Warning messages: 1: In run_pathfindR(data_pathway[1:10, ]) : There already is a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(6)" not to overwrite the previous results. 2: In pathfindR::input_processing(input, p_val_threshold, pin_path, : The gene column was turned into character from factor.

egeulgen commented 5 years ago

Even if you only filter for adj.P.Val > 0, pathfindR initially filters for p <= 0.05 by default. Though, we would recommend against it, you can change this threshold by setting p_val_threshold = 1 when running run_pathfindR.

Because the (by default) 10 iterations of subnetwork search + enrichment is in parallel, the error is usually cryptic stating only task 1 failed. This error is the same for all of the steps in the parallel loop and is not related to your internet connection but thew connection to a parallel R session.

The initial warning states Could not find any interactions for 1 (50%) genes in the PIN so the input for active subnetwork search (basically data_pathway[1:10, ] filtered as p <= 0.05 by pathfindR) contains only 2 genes (1 was found in the protein-protein interaction network and the other wasn't). Because there is only 1 gene in the processed input, the active subnetwork search process fails and each parallel R session throws an error.

I recommend changing the run command to:

output <- run_pathfindR(data_pathway[1:10, ], p_val_threshold = 1)

Meanwhile, I will add a step ensuring that the input data frame is always larger than 1 gene.

Best, -E

engelsdaniel commented 5 years ago

Sorry, but it is still not running. When I set p_val_threshold = 0, there is "no gene found in the PIN". If I define p_val_threshold = 0.01 there are all genes found in the PIN, however, the subnetwork search fails again due to a connectivity problem.

output <- run_pathfindR(data_pathway[1:500, ], p_val_threshold = 0.01)

Testing input

The input looks OK

Processing input. Converting gene symbols, if necessary (and if human gene symbols provied)

Found interactions for all genes in the PIN

Performing Active Subnetwork Search and Enrichment

Error in { : task 1 failed - "kann Verbindung nicht öffnen"

egeulgen commented 5 years ago

hello @adrianleverkuehn, would you mind sharing the input data (data_pathway) as an RDS file so we can try to reproduce the issue?

hernandezvargash commented 4 years ago

Similar issue here. Any help appreciated. I installed with pak::pkg_install("pathfindR") w/o any issues, but get this error when running the example (output_df <- run_pathfindR(RA_input, p_val_threshold = 0.01)): Error in download.file(url, t, quiet = TRUE) : cannot open URL 'https://www.kegg.jp/kegg-bin/show_pathway?hsa03040/hsa%3a9879%09white,black/hsa%3a7919%09white,black/hsa%3a6625%09white,black/hsa%3a6626%09white,black/hsa%3a6631%09white,black/hsa%3a8449%09white,black/hsa%3a9785%09white,black/hsa%3a51362%09white,black/hsa%3a58517%09white,black/hsa%3a1659%09white,black/hsa%3a1665%09white,black/hsa%3a1655%09white,black/hsa%3a10915%09white,black/hsa%3a6627%09white,black/hsa%3a6629%09white,black/hsa%3a22827%09%232FEE2F,black/hsa%3a10285%09white,black/hsa%3a84991%09white,black/hsa%3a10523%09white,black/hsa%3a23350%09white,black/hsa%3a27339%09white,black/hsa%3a988%09white,black/hsa%3a10286%09white,black/hsa%3a5356%09white,black/hsa%3a51503%09white,black/hsa%3a56259%09white,black/hsa%3a10084%09white,black/hsa%3a51729%09white,black/hsa%3a22938%09white,black/hsa%3a51645%09white,black/hsa%3a10450%09white,black/hsa%3a151903%09white,black/hsa%3a55696%09white,black/hsa%3a9716%09white,black/hsa%3a26121%09white,black/hsa%3a10465%09white,bla...

egeulgen commented 4 years ago

@hernandezvargash this issue was resolved in the development version. Please download the dev version via:

pak::pkg_install("egeulgen/pathfindR")
hernandezvargash commented 4 years ago

cool, this is working, thanks a lot!

lucalvizi commented 4 years ago

Hi, I am having this error when

pak::pkg_install("egeulgen/pathfindR") Error: callr subprocess failed: row names contain missing values

could you help me with that please?

Thank you

egeulgen commented 4 years ago

Hey @lucalvizi, This is an issue with pak. I suggest you create an issue there. Meanwhile you can install pathfindR dev version via devtools:

install.packages("devtools") # if you have not installed "devtools"
devtools::install_github("egeulgen/pathfindR")
lucalvizi commented 4 years ago

Many thanks!