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Type 'q()' to quit R. > # test.ISOpureS1.model_optimize.mm_functions.R ##################################### > # Testing script for functions needed in the optimilzation of mm in Step 1 > # Test mm separately since it takes a while... > # > # The functions are of the form ISOpureS1.model_optimize.--- > # (mm) > # mm_loglikelihood > # mm_deriv_loglikelihood > > # LOAD DATA ####################################################################################### > # load library > library(ISOpureR); > > # load the data from that path > data.path <- paste0(file.path(system.file(package = "ISOpureR"), 'extdata', 'Beer')); > load(file.path(data.path , 'beer.tumordata.250.transcripts.30.patients.RData')); > load(file.path(data.path, 'beer.ISOpureS1model.250.transcripts.30.patients.RData')); > > # the normaldata and tumourdata should be matrices > beer.tumordata <- as.matrix(beer.tumordata); > > # TEST MM FUNCTIONS ############################################################################### > > # inputs needed for mm functions > ww <- t(ISOpureS1model$mm_weights); > > # test mm functions > ISOpureS1.model_optimize.mm.mm_loglikelihood(ww, beer.tumordata, ISOpureS1model); [1] 46410717 > ISOpureS1.model_optimize.mm.mm_deriv_loglikelihood(ww, beer.tumordata, ISOpureS1model); [,1] 10_at 0.000000e+00 100_at 3.499203e-03 1000_at -3.831201e-02 10007_at -8.821444e-01 10009_at 1.120788e-01 1001_at -2.610089e-01 10010_at 6.211559e-02 100129762_at 3.372456e-01 100130130_at -2.403702e+00 100131164_at -2.397493e-01 100132596_at 6.621233e-02 100132779_at -3.751592e-01 100133166_at 1.745003e-01 1002_at -7.663040e-01 10024_at 2.633465e-01 10026_at 1.948342e-02 1003_at 1.583364e+00 10036_at 6.350064e-02 1004_at 1.430982e-01 10046_at -3.358346e-01 10059_at 1.834643e-01 1006_at 1.813025e-01 10062_at -3.487887e-01 10063_at 8.901114e-01 10075_at -1.608308e+00 10076_at 3.861781e-01 1009_at 1.522479e-01 10093_at -9.923115e-01 10095_at -4.077054e-01 10099_at 1.547496e-01 101_at -5.836659e-01 1010_at 3.327192e-02 10102_at -2.736347e-01 10105_at -5.087353e-01 10106_at -8.796705e-01 10109_at 5.513025e+00 10111_at -6.329449e-01 10114_at 1.421164e-01 1012_at -7.635784e-02 10120_at -4.047969e-01 10121_at 5.258522e-01 10128_at -1.828815e-02 10129_at 2.004477e-01 1013_at -5.173767e-01 10130_at -4.003672e-01 10131_at 5.473384e-02 10134_at 4.614352e+00 10138_at -8.597589e-01 10139_at 1.652563e+00 10140_at -3.781498e-01 10141_at -2.872632e-01 10142_at 1.561588e-01 10146_at -1.643357e+00 10148_at 2.684320e-01 10149_at 6.228926e-04 1015_at 3.080177e-01 10151_at 3.616845e-02 10152_at -6.659122e-01 10153_at 5.938353e-02 10155_at 1.009533e+00 10158_at -2.676989e-01 1016_at 2.700289e-01 10162_at -1.062978e+00 10165_at -3.190163e-01 10168_at 3.454140e-02 1017_at -2.601031e-01 10180_at -3.240134e-01 10181_at -3.374112e-01 10184_at 3.607351e+00 10188_at 4.098271e-01 1019_at 4.190272e-02 10190_at 4.473520e-01 10195_at 2.707095e-01 10197_at -4.955834e-01 102_at -2.695153e-01 1020_at -1.901878e+00 10200_at 1.199055e-01 10202_at -9.523015e-01 10203_at -2.051215e-02 10204_at 2.819615e+00 10208_at -2.266554e-01 10209_at 8.209660e+00 1021_at -7.982874e-01 10212_at -5.893654e-01 10213_at 5.776414e-02 10215_at 6.945377e-02 10216_at 1.788706e-02 1022_at -1.371684e-01 10221_at 2.551220e-01 10223_at 1.336441e+00 10225_at 2.074900e-01 10227_at 4.199404e-01 10231_at 1.417914e-02 10232_at -3.094057e-01 10233_at -2.389747e-01 10234_at -2.529262e-01 10237_at -3.937510e+00 10238_at -3.349703e-01 10239_at 1.041286e+00 1024_at -3.171038e-01 10240_at -2.172148e-02 10241_at 4.868443e-01 10244_at -2.758042e-01 10246_at 2.752423e-01 10247_at 3.910677e-01 1025_at -1.386694e-01 10255_at -5.538344e-01 1026_at -2.107072e-02 10260_at 2.852994e-01 10265_at -3.483309e-01 10274_at 1.183583e-01 10276_at -8.159437e-01 1028_at 5.248316e-02 10280_at -3.652188e-01 10282_at -1.970741e-01 10284_at -2.104379e-01 10287_at -1.213589e+00 1029_at 8.550521e-01 10291_at 1.504242e+00 10293_at -2.881378e-01 10299_at -2.243668e-01 103_at -5.313070e+00 1030_at -2.511350e-01 10308_at 2.023454e-01 10309_at -2.991270e-01 10312_at -1.773773e+00 10318_at -1.484243e+00 1032_at -2.990482e-01 10320_at 1.324394e-01 10321_at -7.847543e-02 10322_at -5.254127e-01 10325_at 6.653182e-02 10326_at -7.330355e-02 10327_at -3.546510e+00 1033_at -1.663127e-01 10345_at -4.973434e-02 10346_at 9.420533e-01 1036_at -2.546106e-01 10370_at 1.917236e-01 10371_at -1.763611e-01 10379_at 2.219158e+00 1038_at 2.701435e-01 10381_at 1.724418e-01 10382_at -2.020599e+00 10385_at -2.538919e-01 1039_at 2.336872e-01 10397_at 1.304924e+00 10398_at -2.367056e-04 10399_at 3.111341e+00 104_at 1.890439e+00 1040_at 1.231622e-01 10406_at 6.842700e+00 1041_at -1.725820e-01 10413_at -1.411143e-01 10419_at -3.782280e-01 10426_at 9.246678e-02 10428_at -1.839129e-01 1043_at -2.245255e-02 10436_at -2.507859e-01 10437_at -1.058762e-02 10439_at -4.300722e-01 1044_at -3.694645e-01 10440_at -4.931637e-01 10444_at -3.579133e-02 10449_at 3.311711e-01 1045_at -6.626675e-02 10454_at -4.082742e-01 10456_at -3.137191e-01 10457_at -6.388427e-02 10461_at -1.352295e+00 10462_at 4.769387e-01 10468_at -2.678866e-03 10469_at 2.144947e-01 10472_at 8.712683e-02 10473_at -1.429060e-01 10475_at -3.328207e-01 10479_at 3.235180e-02 1048_at 9.410274e-01 10481_at -1.244948e+00 10482_at -6.954951e-01 10483_at 6.040083e-02 10484_at 2.354421e-01 10485_at -8.599688e-01 10487_at 1.787947e-01 10488_at -1.292355e+00 10489_at 9.514036e-01 10493_at -3.482809e-01 10494_at 2.296314e+00 10495_at 4.019305e-01 10499_at -2.146466e-01 1050_at 5.511034e-02 10507_at 1.525935e-01 10512_at -1.990264e-03 10513_at 6.362462e-02 10519_at 3.265456e+00 1052_at 2.668938e-02 10520_at -3.084257e-01 10521_at 1.651885e+00 10523_at 6.503838e+00 10524_at 8.514715e-01 10525_at -2.287561e-01 1053_at -3.024957e-01 10536_at -2.774563e-01 10538_at -6.405040e-01 1054_at 3.453937e-01 10540_at -4.468472e-01 10541_at -2.310276e+00 10544_at -2.650928e-01 10548_at -6.487148e-01 10549_at -3.287443e-01 10552_at -2.953904e+00 10554_at -2.920404e-01 10555_at -2.916488e-01 10556_at -3.405948e-01 10557_at 2.381147e-01 10559_at 6.110651e-02 1056_at -5.006372e-01 10561_at -6.711112e-01 1057_at -1.949899e-01 10573_at 4.013280e-01 10574_at -1.270675e+00 10575_at 4.822016e+00 10576_at 5.115941e-01 10577_at 6.201052e-01 10578_at -8.428878e-01 1058_at 2.405251e-01 10581_at -3.201768e+00 10588_at -2.217321e-02 10589_at -5.739734e-01 1059_at -9.601625e-01 1060_at 5.832010e-02 10606_at -3.586184e-01 10607_at -5.119685e-01 10609_at 1.169983e+00 10610_at 8.789585e-02 10618_at -1.262253e-01 1062_at 2.342352e-01 10623_at -4.517956e-01 10627_at 1.107008e+00 10628_at 1.079984e-01 1063_at -5.922219e-01 10631_at 5.770954e-01 10633_at -6.658496e-01 10634_at -4.678489e-01 10638_at 3.157819e-02 10640_at 5.186179e-01 10643_at -1.249147e+00 10653_at -1.062241e+01 10654_at -1.205578e+00 10657_at 1.780579e-01 > > # remove variables created for this test > rm(ww); > > proc.time() user system elapsed 0.23 0.09 0.31