metastats2.c

   1
   2 #include "metastats.h"
   3
   4 //The following code has been modified using the original Metastats program from White, J.R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352 (2009).
   5
   6 int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int secondGroupingStart){
   7
   8         int size,c=0,i=0,j=0,counter=0, bflag=0;
   9         int B=numPermutations;
  10         int row = numRows;
  11         int col = numCols;
  12         int g = secondGroupingStart;
  13         double thresh=threshold;
  14         double min=0;
  15
  16         char output[1024];
  17         strcpy(output, outputFileName);
  18         FILE *out;
  19
  20         if (g>=col || g<=0){
  21                 printf("Check your g value\n");
  22         }
  23
  24         // Initialize the matrices
  25         size = row*col;
  26         double matrix[row][col];
  27         double pmatrix[size],permuted[size];
  28         double storage[row][9];
  29
  30         for (i=0;i<row;i++){
  31                 for (j =0;j<9;j++){
  32                         storage[i][j]=0;
  33                 }
  34         }
  35
  36         for(i=0; i<row; i++){
  37                 for(j=0; j<col;j++){
  38                         matrix[i][j]=data[i][j];
  39                         pmatrix[c]=0; // initializing to zero
  40                         permuted[c]=0;
  41                         c++;
  42                 }
  43         }
  44
  45         // Produces the sum of each column
  46         double total[col],total1=0,total2=0;
  47         double ratio[col];
  48
  49         for(i=0;i<col;i++){
  50                 total[i]=0;
  51                 ratio[i]=0; }
  52
  53         for(i=0; i<col; i++){
  54                 for(j=0;j<row;j++){
  55                         total[i]=total[i]+matrix[j][i];
  56                 }
  57         }
  58
  59         for(i=0;i<g-1;i++){
  60                 total1=total1+total[i];}
  61
  62         for(i=g-1;i<col;i++){
  63                 total2=total2+total[i];}
  64
  65
  66         // Creates the ratios by first finding the minimum of totals
  67         min = total[0];
  68         if (col==2){
  69                 if (total[0]<total[1]){
  70                         min = total[1];}
  71         }
  72         if (col >2){
  73                 for(i=1;i<col;i++){
  74                         if (min > total[i]){
  75                                 min = total[i];}
  76                 }
  77         }
  78         if (min<=0){
  79                 printf("Error, the sum of one of the columns <= 0.");
  80                 return 0;
  81         }
  82
  83
  84         // Ratio time...
  85         for(i=0;i<col;i++){
  86                 ratio[i]=total[i]/min;
  87         }
  88
  89         // Change matrix into an array as received by R for compatibility.
  90
  91         c=0;
  92         for(i=0;i<col;i++){
  93                 for(j=0;j<row;j++){
  94                         pmatrix[c]=matrix[j][i];
  95                         c++;
  96                 }
  97         }
  98
  99         if(row == 1){
 100                 for (i =0; i<col;i++){
 101                         pmatrix[i]=pmatrix[i]/ratio[i];
 102                 }
 103         }
 104         else {
 105                 counter = 0;
 106                 j=-1;
 107                 for (i=0; i<size; i++) {
 108                         if (counter % row == 0) {
 109                                 j++;
 110                         }
 111                         pmatrix[i]=pmatrix[i]/ratio[j];
 112                         counter++;
 113                 }
 114         }
 115         // pass everything to the rest of the code using pointers. then
 116         // write to output file. below pointers for most of the values are
 117         // created to send everything by reference.
 118
 119         int ptt_size, *permutes,*nc,*nr,*gvalue;
 120
 121         nc = &col;
 122         nr = &row;
 123         gvalue = &g;
 124
 125         permutes = &B;
 126         ptt_size = B*row;
 127
 128         //changing ptt_size to row
 129         double permuted_ttests[row], pvalues[row], tinitial[row];
 130
 131         for(i=0;i<row;i++){
 132                 permuted_ttests[i]=0;}
 133
 134         for(i=0;i<row;i++){
 135                 pvalues[i]=0;
 136                 tinitial[i]=0; }
 137
 138         // Find the initial values for the matrix.
 139         start(pmatrix,gvalue,nr,nc,tinitial,storage);
 140
 141         // Start the calculations.
 142
 143         if ( (col==2) || ((g-1)<8) || ((col-g+1) < 8) ){
 144
 145                 double fish[row], fish2[row];
 146                 for(i=0;i<row;i++){
 147                         fish[i]=0;
 148                         fish2[i]=0;}
 149
 150                 for(i=0;i<row;i++){
 151
 152                         for(j=0;j<g-1;j++){
 153                                 fish[i]=fish[i]+matrix[i][j];
 154                         }
 155
 156                         for(j=g-1;j<col;j++){
 157                                 fish2[i]=fish2[i]+matrix[i][j];
 158                         }
 159
 160                         double  f11,f12,f21,f22;
 161
 162                         f11=fish[i];
 163                         f12=fish2[i];
 164
 165                         f21=total1-f11;
 166                         f22=total2-f12;
 167
 168                         double data[] = {f11, f12, f21, f22};
 169
 170                         // CONTINGENGCY TABLE:
 171                         //   f11   f12
 172                         //   f21   f22
 173
 174                         int *nr, *nc, *ldtabl, *work;
 175                         int nrow=2, ncol=2, ldtable=2, workspace=100000;
 176                         double *expect, *prc, *emin,*prt,*pre;
 177                         double e=0, prc1=0, emin1=0, prt1=0, pre1=0;
 178
 179                         nr = &nrow;
 180                         nc = &ncol;
 181                         ldtabl=&ldtable;
 182                         work = &workspace;
 183
 184                         expect = &e;
 185                         prc = &prc1;
 186                         emin=&emin1;
 187                         prt=&prt1;
 188                         pre=&pre1;
 189
 190                         fexact(nr,nc,data, ldtabl,expect,prc,emin,prt,pre,work);
 191
 192                         if (*pre>.999999999){
 193                                 *pre=1;
 194                         }
 195                         storage[i][8] = *pre;
 196                         pvalues[i]=*pre;
 197                 }
 198         }
 199         else{
 200
 201                 testp(permuted_ttests, permutes, permuted,pmatrix, nc, nr, gvalue,tinitial,pvalues);
 202
 203                 // Checks to make sure the matrix isn't sparse.
 204                 double sparse[row], sparse2[row];
 205                 for(i=0;i<row;i++){
 206                         sparse[i]=0;
 207                         sparse2[i]=0;}
 208
 209                 c=0;
 210                 for(i=0;i<row;i++){
 211
 212                         for(j=0;j<g-1;j++){
 213                                 sparse[i]=sparse[i]+matrix[i][j];
 214                         }
 215
 216                         if(sparse[i] < (double)(g-1)){
 217                                 c++;
 218                         }
 219                         for(j=g-1;j<col;j++){ // ?<= for col
 220                                 sparse2[i]=sparse2[i]+matrix[i][j];
 221                         }
 222
 223                         if( (sparse2[i] <(double)(col-g+1))) {
 224                                 c++;
 225                         }
 226
 227                         if (c==2){
 228                                 c=0;
 229
 230                                 double  f11,f12,f21,f22;
 231
 232                                 f11=sparse[i];
 233                                 sparse[i]=0;
 234
 235                                 f12=sparse2[i];
 236                                 sparse2[i]=0;
 237
 238                                 f21=total1-f11;
 239                                 f22=total2-f12;
 240
 241                                 double data[] = {f11, f12, f21, f22};
 242
 243                                 int *nr, *nc, *ldtabl, *work;
 244                                 int nrow=2, ncol=2, ldtable=2, workspace=10000000; // I added two zeros for larger data sets
 245                                 double *expect, *prc, *emin,*prt,*pre;
 246                                 double e=0, prc1=0, emin1=0, prt1=0, pre1=0;
 247
 248                                 nr = &nrow;
 249                                 nc = &ncol;
 250                                 ldtabl=&ldtable;
 251                                 work = &workspace;
 252
 253                                 expect = &e;
 254                                 prc = &prc1;
 255                                 emin=&emin1;
 256                                 prt=&prt1;
 257                                 pre=&pre1;
 258
 259                                 fexact(nr,nc,data, ldtabl,expect,prc,emin,prt,pre,work);
 260
 261                                 if (*pre>.999999999){
 262                                         *pre=1;
 263                                 }
 264                                 storage[i][8] = *pre;
 265                                 pvalues[i]=*pre;
 266                         }
 267                 }
 268                 // End of else statement
 269                 bflag = 1;
 270         }
 271
 272         // Calculates the mean of counts (not normalized)
 273         double temp[row][2];
 274
 275         for(j=0;j<row;j++){
 276                 for(i=0;i<2;i++){
 277                         temp[j][i]=0;
 278                 }
 279         }
 280
 281         for (j=0;j<row;j++){
 282                 for (i=1; i<=(g-1); i++){
 283                         temp[j][0]=temp[j][0]+matrix[j][i-1];
 284                 }
 285                 temp[j][0]= (double) temp[j][0]/(g-1);
 286                 for(i=g;i<=col;i++){
 287                         temp[j][1]=temp[j][1]+matrix[j][i-1];
 288                 }
 289                 temp[j][1]= (double) temp[j][1]/(col-g+1);
 290         }
 291
 292         for(i=0;i<row;i++){
 293                 storage[i][3]=temp[i][0];
 294                 storage[i][7]=temp[i][1];
 295                 storage[i][8]=pvalues[i];
 296         }
 297
 298         // BACKUP checks
 299
 300         for (i=0;i<row;i++){
 301                 if(pvalues[i]<thresh){
 302                         printf("Feature %d is significant, p = %.10lf \n",i+1,pvalues[i]);
 303                 }
 304         }
 305
 306         // And now we write the files to a text file.
 307         struct tm *local;
 308         time_t t;
 309         t = time(NULL);
 310         local = localtime(&t);
 311
 312         out = fopen(output,"w");
 313
 314         fprintf(out,"Local time and date of test: %s\n", asctime(local));
 315         fprintf(out,"# rows = %d, # col = %d, g = %d\n\n",row,col,g);
 316         if (bflag == 1){
 317                 fprintf(out,"%d permutations\n\n",B);
 318         }
 319
 320         //output column headings - not really sure... documentation labels 9 columns, there are 10 in the output file
 321         //storage 0 = meanGroup1 - line 529, 1 = varGroup1 - line 532, 2 = err rate1 - line 534, 3 = mean of counts group1?? - line 291, 4 = meanGroup2 - line 536, 5 = varGroup2 - line 539, 6 = err rate2 - line 541, 7 = mean of counts group2?? - line 292, 8 = pvalues - line 293
 322         fprintf(out, "OTU\tmean(group1)\tvariance(group1)\tstderr(group1)\tmean_of_counts(group1)\tmean(group2)\tvariance(group2)\tstderr(group2)\tmean_of_counts(group1)\tp-value\n");
 323
 324         for(i=0; i<row; i++){
 325                 fprintf(out,"%d",(i+1));
 326
 327                 for(j=0; j<9;j++){
 328                         fprintf(out,"\t%.12lf",storage[i][j]);
 329                 }
 330                 fprintf(out,"\n");
 331         }
 332
 333         fprintf(out,"\n \n");
 334
 335         // fclose(jobj);
 336         fclose(out);
 337
 338         return 0;
 339 }
 340
 341 void testp(double *permuted_ttests,int *B,double *permuted,
 342                    double *Imatrix,int *nc,int *nr,int *g,double *Tinitial,double
 343                    *ps) {
 344
 345         double Tvalues[*nr];
 346         int a, b, n, j;
 347
 348         a = *B;
 349         b = *nr;
 350         n = a*b;
 351
 352         double counter[b];
 353
 354         for(j=0;j<b;j++){
 355                 counter[j]=0;
 356         }
 357
 358         for (j=1; j<=*B; j++){
 359                 permute_matrix(Imatrix,nc,nr,permuted,g,Tvalues,Tinitial,counter);
 360                 // for(i=0;i<*nr;i++){
 361                 //   permuted_ttests[k]=fabs(Tvalues[i]);
 362                 //    k++;
 363     }
 364
 365
 366         for(j=0;j<*nr;j++){
 367                 ps[j]=((counter[j]+1)/(double)(a+1));
 368         }
 369 }
 370
 371 void permute_matrix(double *Imatrix,int *nc,int *nr,double *permuted,
 372                                         int *g,double *trial_ts,double *Tinitial,double *counter1){
 373
 374         int i=0,j=0,n=0,a=0,b=0,f=0,c=0,k=0;
 375
 376         a = *nr; // number of rows
 377         b = *nc;
 378         n = a*b;
 379
 380         int y[b];
 381
 382         for (i=1; i<=*nc; i++){
 383                 y[i-1] = i;
 384         }
 385
 386         permute_array(y, b);
 387
 388         for (i=0; i<*nc; i++){
 389                 f = y[i]; //column number
 390                 c=1;
 391                 c*=(f-1);
 392                 c*=a;
 393                 if (f == 1){
 394                         c = 0;
 395                 } // starting value position in the Imatrix
 396                 for(j=1; j<=*nr; j++){
 397                         permuted[k] = Imatrix[c];
 398                         c++;
 399                         k++;
 400                 }
 401         }
 402
 403         calc_twosample_ts(permuted,g,nc,nr,trial_ts,Tinitial,counter1);
 404 }
 405
 406 void permute_array(int *array, int n) {
 407         static int seeded = 0;
 408         int i;
 409
 410         if (! seeded) {
 411                 seeded = 1;
 412                 srand(time(NULL));
 413         }
 414
 415         for (i = 0; i < n; i++) {
 416                 int selection = rand() % (n - i);
 417                 int tmp = array[i + selection];
 418                 array[i + selection] = array[i];
 419                 array[i] = tmp;
 420         }
 421 }
 422
 423 void calc_twosample_ts(double *Pmatrix,int *g,int *nc,int *nr,
 424                                            double *Ts,double *Tinitial,double *counter) {
 425         int i,a;
 426         a = *nr;
 427         a*=4;
 428
 429         double C1[*nr][3], C2[*nr][3], storage[a],tool[a];
 430         double nrows,ncols,gvalue, xbardiff=0, denom=0;
 431
 432         nrows = (double) *nr;
 433         ncols = (double) *nc;
 434         gvalue= (double) *g;
 435
 436     meanvar(Pmatrix,g,nr,nc,storage);
 437     for(i=0;i<=a-1;i++){
 438                 tool[i]=storage[i];
 439     }
 440     for (i=0; i<*nr;i++){
 441                 C1[i][0]=tool[i];
 442                 C1[i][1]=tool[i+*nr+*nr];
 443                 C1[i][2]=C1[i][1]/(gvalue-1);
 444
 445                 C2[i][0]=tool[i+*nr];
 446                 C2[i][1]=tool[i+*nr+*nr+*nr]; // var group 2
 447                 C2[i][2]=C2[i][1]/(ncols-gvalue+1);
 448     }
 449
 450     for (i=0; i<*nr; i++){
 451                 xbardiff = C1[i][0]-C2[i][0];
 452                 denom = sqrt(C1[i][2]+C2[i][2]);
 453                 Ts[i]=fabs(xbardiff/denom);
 454                 if (fabs(Ts[i])>(fabs(Tinitial[i])+.0000000000001)){ //13th place
 455                         counter[i]++;
 456                 }
 457     }
 458 }
 459
 460 void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *store){
 461         double temp[*nr], temp2[*nr],var[*nr],var2[*nr],a,b;
 462
 463         int i,m,k,l,n;
 464
 465         a = (double) *g-1;
 466         b = (double) (*nc-a);
 467
 468         for (i = 0; i<*nr; i++){
 469                 temp[i]=0;
 470                 temp2[i]=0;
 471                 var[i]=0;
 472                 var2[i]=0;
 473         }
 474
 475         k = *nr; // number of rows
 476         l = *nc;
 477         n = k*l;
 478
 479     m=0;
 480     m=*g-1;
 481     k=*nr;
 482     m*=k; // m = g * nr now
 483     for (i=0;i<m;i++){
 484                 temp[i%k]=temp[i%k]+pmatrix[i];
 485     }
 486     for (i=0;i<n;i++){
 487                 temp2[i%k]=temp2[i%k]+pmatrix[i];
 488     }
 489     for (i=0;i<*nr;i++){
 490                 temp2[i]=temp2[i]-temp[i];
 491     }
 492     for (i=0;i<=*nr-1;i++){
 493                 store[i]=temp[i]/a;
 494                 store[i+*nr]=temp2[i]/b;
 495     }
 496
 497     // That completes the mean calculations.
 498
 499     for (i=0;i<m;i++){
 500                 var[i%k]=var[i%k]+pow((pmatrix[i]-store[i%k]),2);
 501     }
 502     for (i=m;i<n;i++){
 503                 var2[i%k]=var2[i%k]+pow((pmatrix[i]-store[(i%k)+*nr]),2);
 504     }
 505
 506     for (i=0;i<=*nr-1;i++){
 507                 store[i+2*k]=var[i]/(a-1);
 508                 store[i+3*k]=var2[i]/(b-1);
 509     }
 510     // That completes var calculations.
 511 }
 512
 513 void start(double *Imatrix,int *g,int *nr,int *nc,double *initial,
 514                    double storage[][9]){
 515         int i, a = *nr;
 516         a*=4;
 517
 518         double store[a], tool[a], C1[*nr][3], C2[*nr][3];
 519         double nrows,ncols,gvalue, xbardiff=0, denom=0;
 520
 521         nrows = (double) *nr;
 522         ncols = (double) *nc;
 523         gvalue= (double) *g;
 524
 525         meanvar(Imatrix,g,nr,nc,store);
 526
 527         for(i=0;i<=a-1;i++){
 528                 tool[i]=store[i];
 529         }
 530         for (i=0; i<*nr;i++){
 531                 C1[i][0]=tool[i]; //mean group 1
 532                 storage[i][0]=C1[i][0];
 533                 C1[i][1]=tool[i+*nr+*nr]; // var group 1
 534                 storage[i][1]=C1[i][1];
 535                 C1[i][2]=C1[i][1]/(gvalue-1);
 536                 storage[i][2]=sqrt(C1[i][2]);
 537
 538                 C2[i][0]=tool[i+*nr]; // mean group 2
 539                 storage[i][4]=C2[i][0];
 540                 C2[i][1]=tool[i+*nr+*nr+*nr]; // var group 2
 541                 storage[i][5]=C2[i][1];
 542                 C2[i][2]=C2[i][1]/(ncols-gvalue+1);
 543                 storage[i][6]=sqrt(C2[i][2]);
 544         }
 545         for (i=0; i<*nr; i++){
 546                 xbardiff = C1[i][0]-C2[i][0];
 547                 denom = sqrt(C1[i][2]+C2[i][2]);
 548                 initial[i]=fabs(xbardiff/denom);
 549         }
 550 }
 551
 552
 553
 554