Got error while running PUMA through netZooR

[kr-swapnil]

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

[marouenbg]

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

[kr-swapnil]

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]

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]

Thanks for your patience @kr-swapnil , the issue has now been fixed in #310
You can reinstall netZooR from the devel branch

[marouenbg]

Please let me know if you need anything else.
Marouen