C++ demo for Mutual Rank based co-expression hub/module identification
MRCT is a program could find hub structure and coexpression module.
More information related the method, see this link.
For the R codes which could reproduce the result of “MRHCA: A nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network”, see this link.
git clone --recursive https://github.com/zy26/mrct.gitcd mrct/
Or, you can just click Clone or download under the repository name, then put the code files of libmrct to lib dir.
You may need g++ version >= 5.40.
g++ -std=c++14 -fopenmp -O3 lib/*.cc src/*.cc
./a.out -i testdata/E_coli_anaerobic.txt -o E_coli_anaerobic.id.txt -e E_coli_anaerobic.mr.txt -t 0.9
Use Visual Studio project file mrct.vcxproj inside. You may need modify the Platform Toolset to the version on your PC (You will need Visual Studio 2019 or higher to allow unsigned int for the OpenMP loop counter).
The Command Arguments should be -i testdata/E_coli_anaerobic.txt -o E_coli_anaerobic.id.txt -e E_coli_anaerobic.mr.txt -t 0.9, or you can use your file name instead.
Warning: Try to avoid Debug mode, it may be very slow.
You will see the content of the first output file (E_coli_anaerobic.id.txt) as below somehow.
1 0 1639 979 b33851 0 1589 1232 b04211 0 1583 2167 b36491 0 1559 535 b01841 0 1549 3789 b45571 0 1547 2562 b38331 0 1532 2777 b04341 0 1528 960 b35601 0 1520 2837 b06371 0 1512 2115 b37041 0 1506 3861 b39991 0 1501 13 b32551 0 1496 1880 b42011 0 1481 698 b26101 0 1480 2425 b38381 0 1462 2112 b01831 0 1458 1049 b39971 0 1447 496 b36391 0 1433 2103 b09531 0 1426 1099 b43721 0 1417 1335 b32001 0 1414 2032 b36201 0 1409 2521 b29601 0 1406 566 b36401 0 1406 2113 b06101 0 1406 2133 b39851 0 1395 2489 b30351 0 1392 2520 b36511 0 1386 3769 b36111 0 1382 1340 b01791 0 1374 3770 b36141 0 1365 2066 b37831 0 1367 3727 b34991 0 1359 992 b36101 0 1344 1480 b17821 0 1342 2836 b06361 0 1340 2176 b33411 0 1330 1894 b18311 0 1325 1234 b27471 0 1315 2183 b33071 0 1315 4185 b27921 0 1314 2519 b26071 0 1314 823 b27481 0 1310 2126 b39841 0 1305 2134 b39831 0 1301 2181 b33421 0 1293 1694 b39821 0 1289 1305 b28281 0 1284 1551 b09231 0 1282 801 b01721 0 1273 1236 b27461 0 1265 197 b37341 0 1254 2336 b36411 0 1253 203 b37331 0 1245 4267 b42121 0 1232 204 b37351 0 1230 2784 b04711 0 1228 1336 b32011 0 1234 3746 b35521 0 1208 2539 b01701 0 1198 3592 b29531 0 1200 3104 b14471 0 1188 3498 b26431 0 1179 4245 b31991 0 1175 2204 b01761 0 1170 2146 b33181 0 1174 2292 b39811 0 1162 1828 b38211 0 1164 2030 b36191 0 1160 1762 b23201 0 1171 3606 b29861 0 1136 2535 b27451 0 1124 846 b33401 0 1139 1048 b38041 0 1134 2427 b44831 0 1119 2849 b06991 0 1116 2122 b36431 0 1121 2972 b10341 0 1101 4243 b31951 0 1087 3788 b37051 0 1078 1854 b42261 0 1077 3285 b19781 0 1086 2168 b28301 0 1070 3603 b29831 0 1068 2932 b08981 0 1052 969 b20291 0 1077 3231 b18031 0 1051 3736 b35271 0 1025 4242 b31941 0 1016 363 b06241 0 1030 1900 b03311 0 979 3328 b21221 0 977 4175 b26471 0 969 3417 b23581 139 0 2013 b37001 0 972 3416 b23571 0 977 2742 b02851 0 975 1477 b11751 0 937 1158 b24901 0 942 277 b19871 0 924 4176 b26501 0 951 1534 b21131 0 932 2528 b12651 0 896 2875 b07181 0 933 2034 b38421 0 876 2060 b39011 0 881 2811 b05211 0 853 3421 b23621 372 0 2233 b10121 0 901 1252 b35261 0 848 2640 b20471 0 840 809 b38971 0 836 3536 b27701 0 844 4094 b15851 0 885 1825 b26481 0 865 1253 b18271 364 0 3073 b13601 131 0 2612 b19141 0 834 3032 b12511 0 813 340 b29331 293 0 2302 b29131 0 816 2639 b20501 0 849 3835 b38781 0 819 1757 b34031 0 840 3196 b17241 183 0 3244 b18321 324 0 2747 b02911 135 0 3007 b11791 289 0 1570 b07501 0 801 2865 b07191 308 0 1295 b00751 0 805 3190 b16981 0 791 2727 b02671 0 799 1801 b41051 373 0 3535 b27691 291 0 1443 b30081 0 792 661 b17011 357 0 2746 b02901 315 0 3418 b23591 0 786 3078 b14071 0 779 4171 b25471 0 781 3629 b30801 221 0 2455 b21031 288 0 127 b31721 0 779 3415 b23561 0 781 2307 b19751 0 781 3913 b41831 0 773 2952 b09411 0 784 2467 b00021 374 0 1248 b31371 371 0 3912 b41821 253 0 121 b28181 247 0 126 b02731 318 0 3385 b22941 0 768 2859 b06821 368 0 122 b39591 0 768 2647 b20611 231 0 1194 b00771 201 0 123 b39581 367 0 1730 b13921 211 0 2463 b21041 214 0 1290 b00741 0 761 153 b07541 304 0 1727 b13891 0 738 795 b44741 346 0 3456 b25061 228 0 167 b08601 218 0 1193 b00781 325 0 7 b13381 177 0 1957 b13021 0 738 359 b20481 254 0 2085 b10661 209 0 158 b01121 0 736 4017 b45721 233 0 1293 b00711 207 0 2459 b39901 223 0 2526 b12631 236 0 1639 b36611 219 0 1444 b38291 237 0 1292 b00721 233 0 3626 b30741 210 0 889 b17611 239 0 124 b33591 309 0 2642 b20441 212 0 376 b10401 199 0 1441 b40131 202 0 1291 b00731 206 0 378 b10381 224 0 129 b42541 220 0 3582 b29301 218 0 2523 b12601 141 0 2939 b09061 136 0 665 b20971 131 0 2420 b1519
That means: We find 194 hubs.
The second column is the cluster bound of the cluster.
The third column is a upper bound of the cluster.
The forth column is the index of the original rows in the matrix of the input file.
The last column is the row names of the forth column.
We can use the R package fix the thrid column later.
We have another output file, the first column in it is the same as the forth column of the file below.
Other columns are the EM values for that row.