Closed kr-swapnil closed 6 months ago
Hi @kr-swapnil, Happy new year! Would you mind sharing a working example I can reproduce?
Hi, Happy new year! I have attached the required input files and command to reproduce the error.
Input sample files:
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")
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.
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
Please let me know if you need anything else. Marouen
PUMA run Error in seq.default(1, num.TFs * num.TFs, num.TFs + 1) : wrong sign in 'by' argument. How to solve this?