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EA2106-Universite-Francois-Rabelais / Expression-network-analysis

C and R codes to decipher transcriptional associations
http://bbv-ea2106.sciences.univ-tours.fr/
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HRR_cut.R number of rows #2

Closed cascoamarillo closed 3 years ago

cascoamarillo commented 3 years ago

Hi,

I have some issues coming after getting the vectors (hrr) and calling HRR_cut.R for processing them. My doubt is with the options -s, -S and -c from HRR_cut.R, if am I doing it right: `-s INTEGER, --size=INTEGER Number of rows in the processed matrix (not REAL size), see hrr standard output

    -S INTEGER, --realsize=INTEGER
        Number of rows in the matrix (REAL size), see hrr standard output

    -c INTEGER, --subsize=INTEGER
        Number of row in the submatrix, see hrr standard output`

I get some errors coming from it, like NULL Error: unexpected end of input Execution halted

So I am going to place here my data and see if someone can chime in. Thanks in advance:

My data file is and RNAseq reads count matrix; pretty simple: 18760 transcripts and 6 conditions $ head TagSeqExample.dat T1a T1b T2 T3 N1 N2 Gene_00001 0 0 2 0 0 1 Gene_00002 20 8 12 5 19 26 Gene_00003 3 0 2 0 0 0 Gene_00004 75 84 241 149 271 257 Gene_00005 10 16 4 0 4 10 Gene_00006 129 126 451 223 243 149 Gene_00007 13 4 21 19 31 4 Gene_00008 0 3 0 0 0 0 Gene_00009 202 122 256 43 287 357

For hrr I used mpirun -np 4 ./hrr ../TagSeqExample.dat rankmatrix doubleprecision

All good: four vector files.txt. Then created a folder, like PCC_lt, moved there the 4 .txt vector files. Before that, this is the output from hrr:

mpirun -np 4 ./hrr ../TagSeqExample.dat rankmatrix doubleprecision -- start -- -- start -- -- start -- -- start -- args (rankmatrix) args (doubleprecision) args (rankmatrix) args (doubleprecision) procs: [4] rank: [1] inputfile: [../TagSeqExample.dat] localsave: [0] args (rankmatrix) args (doubleprecision) procs: [4] rank: [2] inputfile: [../TagSeqExample.dat] localsave: [0] args (rankmatrix) args (doubleprecision) procs: [4] rank: [3] inputfile: [../TagSeqExample.dat] localsave: [0] procs: [4] rank: [0] inputfile: [../TagSeqExample.dat] localsave: [0] bench_file: gen_size: 18764 data_size: 6 real_gen_size: 18760 RANK: 0: broadcasting data RANK: 1: receiving dim: 18764 6: allocated size: 450336 RANK: 1: broadcasting data RANK: 2: receiving dim: 18764 6: allocated size: 450336 RANK: 2: broadcasting data RANK: 3: receiving dim: 18764 6: allocated size: 450336 RANK: 3: broadcasting data RANK: 0: receiving dim end: 18764 6 RANK: 1: receiving dim end: 18764 6 RANK: 2: receiving dim end: 18764 6 RANK: 3: receiving dim end: 18764 6 RANK: 0: build_rank_matrix start 4691 18764 RANK: 2: build_rank_matrix start 4691 18764 RANK: 1: build_rank_matrix start 4691 18764 RANK: 3: build_rank_matrix start 4691 18764 RANK: 1: build_rank_matrix end RANK: 1: process_max_hrr: procs 4 gen_size: 18764 data_size: 6 gen_sub_size: 4691 RANK: 2: build_rank_matrix end RANK: 2: process_max_hrr: procs 4 gen_size: 18764 data_size: 6 gen_sub_size: 4691 RANK: 0: build_rank_matrix end RANK: 0: process_max_hrr: procs 4 gen_size: 18764 data_size: 6 gen_sub_size: 4691 RANK: 3: build_rank_matrix end RANK: 3: process_max_hrr: procs 4 gen_size: 18764 data_size: 6 gen_sub_size: 4691 RANK: 2: process_max_hrr END RANK: 2 save_all_result: 88021924 18764 4691 RANK: 0: process_max_hrr END RANK: 0 save_all_result: 88021924 18764 4691 RANK: 0: save data to disk: start (0.txt) RANK: 1: process_max_hrr END RANK: 1 save_all_result: 88021924 18764 4691 RANK: 3: process_max_hrr END RANK: 3 save_all_result: 88021924 18764 4691 RANK: 0: save data to disk: end RANK: 1: save data to disk: start (1.txt) RANK: 1: save data to disk: end RANK: 2: save data to disk: start (2.txt) RANK: 2: save data to disk: end RANK: 3: save data to disk: start (3.txt) RANK: 3: save data to disk: end Now, for running HRR_cut.R into /PCC_lt folder, I started using HRR_cut.R -n 4 -a ../TagSeqExample.ids -s 18764 -S 18760 -c 4691 -r PCC -m 4

According to hhr output; bench_file: gen_size: 18764 data_size: 6 real_gen_size: 18760 ... RANK: 1: process_max_hrr: procs 4 gen_size: 18764 data_size: 6 gen_sub_size: 4691

I used: gen_size: 18764, as -s "Number of rows in the processed matrix (not REAL size)" real_gen_size: 18760, as -S "Number of rows in the matrix (REAL size)" gen_sub_size: 4691, as -c "Number of row in the submatrix"

BUT, something is not right. I have tried to change this numbers to other potential candidates, but nothing works, Maybe I misinterpreted the documentation? Although, I get some output results: $ head Gene_00001 "lt" "corr" "1" "Gene_00001" 0 "2" "Gene_00002" 8774 "3" "Gene_00003" 7775 "4" "Gene_00004" 5345 "5" "Gene_00005" 11558 "6" "Gene_00006" 4687 "7" "Gene_00007" 12862 "8" "Gene_00008" 12811 "9" "Gene_00009" 5828 $ tail Gene_00001 "18755" "Gene_18755" 5189 "18756" "Gene_18756" 8697 "18757" "Gene_18757" 6017 "18758" "Gene_18758" 7630 "18759" "Gene_18759" 11019 "18760" "Gene_18760" 9392 "18761" "Gene_18760" 9392 "18762" "Gene_18760" 9392 "18763" "Gene_18760" 9392 "18764" "Gene_18760" 9392

Btw, TagSeqExample.ids is just one column with ids, right?: $ head TagSeqExample.ids Gene_00001 Gene_00002 Gene_00003 Gene_00004 Gene_00005 Gene_00006 Gene_00007 Gene_00008 Gene_00009 Gene_00010

EA2106-Universite-Francois-Rabelais commented 3 years ago

Hi @cascoamarillo , thanks for your interest for this program. I have an updated version of the R script to collect the best coexpressed gene pairs. I will post it as soon as possible!

cascoamarillo commented 3 years ago

Thanks for the quick reply! Looking forward to it.

EA2106-Universite-Francois-Rabelais commented 3 years ago

I updated the code. It now works with a full bash script to calculate the HRR and extract the best pairs. Please do not hesitate to contact me if you have any problem with it. I also updated the hrr.tgz, I think you should download and recompile it. Good luck!

cascoamarillo commented 3 years ago

Yes, it nicely works! Thank you. Now trying to understand how igraph works. Closing.

EA2106-Universite-Francois-Rabelais commented 3 years ago

I will post some tips...

De: "cascoamarillo" notifications@github.com À: "EA2106-Universite-Francois-Rabelais/Expression-network-analysis" Expression-network-analysis@noreply.github.com Cc: "Thomas Duge De Bernonville" thomas.duge@univ-tours.fr, "Comment" comment@noreply.github.com Envoyé: Vendredi 8 Janvier 2021 16:42:20 Objet: Re: [EA2106-Universite-Francois-Rabelais/Expression-network-analysis] HRR_cut.R number of rows (#2)

Yes, it nicely works! Thank you. Now trying to understand how igraph works. Closing.

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