Calculates some indicators for each node in the network.
# S4 method for omics_network
analyze_network(Omega, nv, label_v = NULL)a omics_network object
the level of cutoff at which the analysis should be done
(optionnal) the name of the genes
A matrix containing, for each node, its betweenness,its degree, its output, its closeness.
data(network)
analyze_network(network,nv=0)
#> Loading required package: tnet
#> Loading required package: igraph
#>
#> Attaching package: ‘igraph’
#> The following object is masked from ‘package:Patterns’:
#>
#> compare
#> The following object is masked from ‘package:DynDoc’:
#>
#> path
#> The following objects are masked from ‘package:stats’:
#>
#> decompose, spectrum
#> The following object is masked from ‘package:base’:
#>
#> union
#> Loading required package: survival
#> tnet: Analysis of Weighted, Two-mode, and Longitudinal networks.
#> Type ?tnet for help.
#> node betweenness degree output closeness
#> 1 1 198 45 0.469801103 115.903327
#> 2 2 25 72 0.638928759 83.063082
#> 3 3 4 45 0.650350027 87.061645
#> 4 4 246 56 1.568438860 163.897602
#> 5 5 296 29 0.800405535 147.300670
#> 6 6 22 50 0.631385634 84.830824
#> 7 7 105 40 0.510093629 79.058898
#> 8 8 0 60 0.831951787 101.310557
#> 9 9 773 71 2.467857820 167.135446
#> 10 10 888 73 3.752542041 237.684494
#> 11 11 21 57 1.216543820 181.215213
#> 12 12 112 56 1.204054063 125.028827
#> 13 13 407 58 1.036650559 152.029315
#> 14 14 3 62 0.692952694 85.174289
#> 15 15 1039 56 3.065983757 304.121187
#> 16 16 742 74 3.235406870 236.643385
#> 17 17 418 50 2.008931860 164.416975
#> 18 18 809 43 2.206203179 179.319850
#> 19 19 0 51 0.356455321 59.224482
#> 20 20 0 63 0.549960963 75.273850
#> 21 21 0 1 0.004475704 11.784278
#> 22 22 20 12 0.326518633 98.918177
#> 23 23 0 4 0.006311850 13.858663
#> 24 24 0 0 0.000000000 0.000000
#> 25 25 0 2 0.003019120 7.967493
#> 26 26 186 17 0.095327608 58.848089
#> 27 27 0 33 0.103882029 67.490555
#> 28 28 0 0 0.000000000 0.000000
#> 29 29 0 4 0.056228783 44.016148
#> 30 30 5 10 0.080530134 52.944496
#> 31 31 0 1 0.001812159 6.022486
#> 32 32 0 14 0.074665588 44.828983
#> 33 33 5 8 0.062549930 62.001987
#> 34 34 0 8 0.059090818 56.083944
#> 35 35 1 12 0.142198183 57.742597
#> 36 36 0 0 0.000000000 0.000000
#> 37 37 8 22 0.147872753 57.477842
#> 38 38 21 14 0.223497302 79.456869
#> 39 39 34 26 0.235247646 79.539121
#> 40 40 163 17 0.218449765 95.667232
#> 41 41 11 31 0.211050541 47.312104
#> 42 42 0 22 0.147475862 54.350118
#> 43 43 157 25 0.444488091 139.014044
#> 44 44 176 54 1.026959490 113.149468
#> 45 45 0 8 0.067746335 19.094448
#> 46 46 88 31 1.090647718 94.468427
#> 47 47 52 28 0.636401761 90.551082
#> 48 48 213 35 1.215864042 157.955686
#> 49 49 2253 28 2.158005039 381.339329
#> 50 50 207 30 0.593429905 124.064291
#> 51 51 95 17 0.270615619 95.422431
#> 52 52 28 14 0.188128159 76.876138
#> 53 53 193 38 0.582344605 159.650711
#> 54 54 235 39 1.300831276 198.432375
#> 55 55 0 14 0.178093932 56.611717
#> 56 56 0 2 0.003466005 9.857721
#> 57 57 209 44 1.137639574 158.013782
#> 58 58 10 10 0.252058512 71.745032
#> 59 59 0 11 0.099769365 71.996771
#> 60 60 131 26 0.570673015 87.123197
#> 61 61 157 13 0.389970191 145.794189
#> 62 62 8 13 0.115549109 83.426632
#> 63 63 237 22 0.602373931 180.845454
#> 64 64 1148 56 1.772280889 216.238265
#> 65 65 137 18 0.332703885 123.852149
#> 66 66 100 15 0.105998249 50.620088
#> 67 67 1543 79 6.239688253 304.769647
#> 68 68 56 24 0.659225438 94.288606
#> 69 69 1158 72 7.977272772 392.362109
#> 70 70 666 70 4.786608465 261.311430
#> 71 71 386 36 1.107687884 140.438332
#> 72 72 0 22 0.206933486 84.004642
#> 73 73 0 14 0.154691176 63.244716
#> 74 74 211 15 0.374471030 135.022274
#> 75 75 0 9 0.048956963 57.009683
#> 76 76 478 47 1.518954643 155.919879
#> 77 77 16 30 0.190685214 85.305500
#> 78 78 9 32 0.496323653 79.570820
#> 79 79 226 33 0.777078748 138.700507
#> 80 80 26 6 0.159098923 93.626341
#> 81 81 294 80 4.015011946 203.802868
#> 82 82 323 25 0.653477617 155.237365
#> 83 83 133 14 0.411038467 151.457804
#> 84 84 2 43 0.497062676 107.920114
#> 85 85 0 8 0.102135477 67.458958
#> 86 86 111 37 0.669546198 109.378041
#> 87 87 4 12 0.106633622 64.731765
#> 88 88 234 61 1.366375255 135.747187
#> 89 89 27 26 0.496320464 131.725455
#> 90 90 83 34 0.945657952 106.538998
#> 91 91 0 5 0.014670192 12.148342
#> 92 92 191 22 0.219192961 93.349440
#> 93 93 208 24 0.278074176 158.180808
#> 94 94 163 32 0.736480926 147.682661
#> 95 95 13 10 0.206570745 115.393984
#> 96 96 1204 80 7.977096594 378.317855
#> 97 97 1 20 0.221063915 100.834754
#> 98 98 185 52 0.848957484 102.243228
#> 99 99 0 32 0.168140838 65.515421
#> 100 100 486 63 2.619433306 157.529780
#> 101 101 114 31 0.703401123 236.998887
#> 102 102 434 58 1.549953727 173.419637