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netZoo / netZooR

netZooR is a network biology package implemented in R.
https://netzoo.github.io/
GNU General Public License v3.0
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Got error while running PUMA through netZooR #309

Closed kr-swapnil closed 6 months ago

kr-swapnil commented 8 months ago

PUMA run Error in seq.default(1, num.TFs * num.TFs, num.TFs + 1) : wrong sign in 'by' argument. How to solve this?

marouenbg commented 8 months ago

Hi @kr-swapnil, Happy new year! Would you mind sharing a working example I can reproduce?

kr-swapnil commented 8 months ago

Hi, Happy new year! I have attached the required input files and command to reproduce the error.

Input sample files:

  1. miRNA-target sample_miR_target.txt
  2. Gene expression sample_gexpr.txt
  3. miRNA list sample_miR_list.txt

Command: mir.tar = read.table("sample_miR_target.txt", head=T) tmp.expr = read.table("sample_gexpr.txt", head=T) mir.list = read.table("sample_miR_list.txt", head=T)

puma.res = puma(motif = mir.tar, expr = tmp.expr, ppi = NULL, alpha = 0.1, mir_file = mir.list$x, iter = 1000, output = "regulatory", progress = TRUE, randomize = "within.gene", edgelist = TRUE, mode = "intersection")

marouenbg commented 8 months ago

Thank you @kr-swapnil! Happy new year to you as well! I am sorry this took too long, if you can work with the MATLAB version https://github.com/netZoo/netZooM/blob/master/netZooM/puma/RunPUMA.m until we get this fixed, otherwise I will get back to you as soon as I can.

marouenbg commented 7 months ago

Thanks for your patience @kr-swapnil , the issue has now been fixed in https://github.com/netZoo/netZooR/pull/310 You can reinstall netZooR from the devel branch

marouenbg commented 6 months ago

Please let me know if you need anything else. Marouen