www.pudn.com > tpWY.rar > one_sided_tpWY.c

/* This program implements the permutation algorithm for the Westfall step-down
   adjusted p-values for the t-statistics for one-sided alternative hypotheses. */

/* Created: Tue Oct 24 15:54:19 EDT 2000 */
/* Elisabetta Manduchi, CBIL, Penn Center for Bioinformatics */

#include 
#include 
#include 
#include "stat_util.h"
#include 

/* argv[1]: if 1 tests for group 2 up-regulated vs group 1, 
            if -1 tests for group 2 down-regulated vs group 1.
/* argv[2]: input file name. */
/* argv[3]: output file name. */
/* argv[4]: number of rows in the input file. */
/* argv[5]: total number of columns in the input file (the first column 
            should contain identifiers [up to 20 characters each] and should
            be separated by 1 tab from the next column). This number includes
            the indentifier column. */
/* argv[6]: number of columns in first group (in the input file these should
            precede the columns in the second group). */
/* argv[7]: the value (float) used to denote missing values */
/* argv[8]: can be 0 or 1; if set to 1, p-values are also computed. */
/* argv[9]: can be 0 or 1; if set to 1, all rearrangements are considered.
            This argument is ignored if argv[8]=0. */
/* argv[10]: number of rearrangements to use in the p-values calculation. 
             If this number is greater than the number of all possible 
             rearrangements, then all rearrangements are considered. This 
             argument is ignored when argv[8]=0 or when argv[9]=1. */

FILE *ofh;
char **id;
float **data, *arr1, *arr2,  *t_arr, *p, *adj_p, *t, *u, na;
int test, do_p, num_rows, num_cols, num_gp1, *gp1, *rest, B, B_new, *indx;

void mallocate();
int cmp(const void *v1, const void *v2);
void compute_t();
void print1();
void print2();
void read_infile(char *filename);
void simulation1();
void simulation2();
int update_p();

main(int argc, char *argv[]) {
  char *infile, *outfile;
  int do_all, c;
  time_t duration, start=time(0);


  if (argc < 8) { 
    fprintf(stderr,"Must provide at least 8 command line arguments in the following order:\n1 or -1 according to the kind of one-tailed hypothesis you want to consider\ninput file name\noutput file name\nnumber of rows in the input file\nnumber of columns in the input file\nnumber of columns in first group\nthe float used to denote missing values\n0 if p-values should not be computed, 1 otherwise\n");
    exit(1);
  }  

  test = atoi(argv[1]);
  if (test!=1 && test!=-1) {
    fprintf(stderr, "The first argument should be either 1 or -1.\n");
    exit(1);
  }
  infile = argv[2];
  outfile = argv[3];
  num_rows = atol(argv[4]);
  num_cols = atoi(argv[5]);
  num_gp1 = atoi(argv[6]);
  na = (float)atof(argv[7]);
  do_p = atoi(argv[8]);
  if (do_p==1 && argc<10) {
    fprintf(stderr, "Must specify whether to consider all rearrangements or not.\n");
    exit(1);
  }
  if (do_p==1) {
    do_all = atoi(argv[9]);
  }
  if (do_p==1 && do_all==0 && argc<11) {
    fprintf(stderr, "Must provide the number of rearrangements to use in the p-values calculation.\n");
    exit(1);
  }
  if (do_p==1 && do_all==0) {
    B = atoi(argv[10]);
    if (B>=bicoeff(num_cols-1, num_gp1)) {
      do_all = 1;
      fprintf(stderr, "Since the number of desired rearrangements is greater than or equal to the number\nof all possible rearrangements, all possible rearrangements are employed.\n");
    }
  }
  if ((ofh=fopen(outfile,"w")) == NULL) {
    fprintf(stderr,"Cannot open %s for writing\n", outfile);
    exit(1);
  } 

  mallocate();
  read_infile(infile);
  compute_t();

  for (c=0; ctest*(*(t_arr+*(int *)v2)))
    return -1;
  else
    return 0; 
}

void compute_t() {
  int i, j;

  for (i=0; i=1) {
      *(adj_p+*(indx+i)) = (*(adj_p+*(indx+i))>=*(adj_p+*(indx+i-1))) ? *(adj_p+*(indx+i)) : *(adj_p+*(indx+i-1));
    }

  }
}

void simulation2() {
  int i, j, h;
  long seed = -time(0);

  B_new = B;
  /* fprintf(stderr, "here1\n"); */
  for (i=0; i=1) {
      *(adj_p+*(indx+i)) = (*(adj_p+*(indx+i))>=*(adj_p+*(indx+i-1))) ? *(adj_p+*(indx+i)) : *(adj_p+*(indx+i-1));
    }
  }
}

int update_p() {  
  int i, j, flag=0;

  for (i=0; i=test*(*(t_arr+i))) {
	*(p+i) += 1;
      }
    }   
    *(u+num_rows-1) = *(t+*(indx+num_rows-1));
    if (test*(*(u+num_rows-1))>=test*(*(t_arr+*(indx+num_rows-1))))
      *(adj_p+*(indx+num_rows-1)) += 1;
    for (i=num_rows-2; i>=0; i--) {
      *(u+i) = (test*(*(u+i+1))>= test*(*(t+*(indx+i)))) ? *(u+i+1) : *(t+*(indx+i));
      if (test*(*(u+i))>=test*(*(t_arr+*(indx+i))))
	*(adj_p+*(indx+i)) += 1;
    }
  }
  return flag;
}