/* ********************************************************************************* *
* write_outfile *
* ------------- *
* Descriptions: *
* write the test-statistics, unadjusted p-values, adjusted pvalues and Adjusted *
* p-values lower to the file. *
* input parameters: *
* filename: the file to write *
* pdata: the pointer of the whole data *
* T,P,Adj_P,Adj_Lower: the array stores the test-statistics, *
* unadjusted p-values, adjusted pvalues and adjusted p-values lower, respectively *
* if Adj_Lower==NULL, it will not print this item *
* *
* ********************************************************************************* */
void write_outfile(FILE *fh, GENE_DATA *pdata, double *T, double *P, double *Adj_P, double *Adj_Lower)
{
int i, nrow;
// Double num,denum
// The length of the array T,P,etc.
nrow=pdata->nrow;
if(myDEBUG)
{
fprintf(stderr, "\nThe results of T,P Adj_P and Adj_Lower");
print_farray(stderr, T, nrow);
print_farray(stderr, P, nrow);
print_farray(stderr, Adj_P, nrow);
if(Adj_Lower)
print_farray(stderr, Adj_Lower, nrow);
}
fprintf(stderr, "\nWe're writing the output\n");
fprintf(fh, "%20s %10s %10s %10s", "gene_id", "test-stat", "unadj-p", "adjusted-p");
if(Adj_Lower)
fprintf(fh, "%10s", "p-lower");
fprintf(fh, "\n");
for (i=0; i<nrow; i++) {
// t_stat_num_den(pdata->d[i],pdata->L, pdata->ncol,pdata->na,&num,&denum);
fprintf(fh, "%20s %10.6f %7g %7g", pdata->id[i], T[i], P[i], Adj_P[i]);
if(Adj_Lower){
fprintf(fh," %7g", Adj_Lower[i]);
}
fprintf(fh, "\n");
}
}
/*get all the samples of T and they're also ordered.It's used only for diagonsis*/
void get_all_samples_T(float* V, int n,float* T,float na,
FUNC_STAT func_stat,FUNC_SAMPLE func_first_sample,
FUNC_SAMPLE func_next_sample,const void* extra)
{
int *L,*R,is_next,b=0,B;
B=(*func_first_sample)(NULL);
/*allocate the spaces*/
assert(L=(int*)Calloc(n,int));
assert(R=(int*)Calloc(B,int));
/*compute all the test_stat*/
(*func_first_sample)(L);
is_next=1;
while(is_next){
T[b]=func_stat(V,L,n,na,extra);
b++;
is_next=(*func_next_sample)(L);
}
if(B!=b){
fprintf(stderr,"Error we have b(%d)!=B(%d)\n",b,B);
return;/*exit(1)*/;
}
if(myDEBUG)
print_farray(stderr,T,B);
Free(L);
Free(R);
}
/* Descriptions: Try to get all the unadjusted p-values for a gene with
experssion values at V with n experiemtns.
int first_sample(int *L)
get the first sample of the labelling.
if L==NULL, then it returns all the possible simulations, which depends on
the initial function create_sampling.
int next_sample(int* L)
get the next sample, if it's done all the sampling, then it returns 0,
otherwise it returns 1.
output is P*/
void get_all_samples_P(float* V, int n,float* P,float na,
FUNC_STAT func_stat,FUNC_SAMPLE func_first_sample,
FUNC_SAMPLE func_next_sample,FUNC_CMP func_cmp,const void* extra)
{
int *L,*R,i,oldb,is_next,b=0,B_new,B;
float* T=P,oldf;/*it first stores T, then switch to P*/
B=(*func_first_sample)(NULL);
/*allocate the spaces*/
assert(L=(int*)Calloc(n,int));
assert(R=(int*)Calloc(B,int));
/*compute all the test_stat*/
(*func_first_sample)(L);
is_next=1;
B_new=0;
while(is_next){
T[b]=func_stat(V,L,n,na,extra);
if(T[b]!=NA_FLOAT)
B_new++;
b++;
is_next=(*func_next_sample)(L);
}
if(B!=b){
fprintf(stderr,"Error we have b(%d)!=B(%d)\n",b,B);
return;/*exit(1)*/;
}
if(myDEBUG)
print_farray(stderr,T,B);
/*order the test_stat*/
order_data(T,R,B,func_cmp);
/*note the last elements of B-B_new has NA T-value*/
/*assign the probabilites*/
oldb=0;
oldf=T[R[0]];
for(b=1;b<B_new;b++){
if((func_cmp==cmp_high)&(T[R[b]]>=oldf-EPSILON)) continue;
else if ((func_cmp==cmp_low ) &&(T[R[b]]<=oldf+EPSILON)) continue;
else if((func_cmp==cmp_abs )&& fabs(T[R[b]])>=fabs(oldf)-EPSILON) continue;
for(i=oldb;i<b;i++)
P[R[i]]=(b+0.0)/B_new;
oldb=b;
if(b<B_new-1) oldf=T[R[b]];
}
for(i=oldb;i<b;i++)
P[R[i]]=1.0;
/*for NA test_stat, assign NA probabilites*/
for(b=B_new;b<B;b++)
P[R[b]]=NA_FLOAT;
/*free the space*/
Free(L);
Free(R);
}
void adj_pvalue_quick(GENE_DATA* pdata,float*T, float* P,
float* Adj_P,float* Adj_Lower,
FUNC_STAT func_stat,FUNC_STAT func_stat_T,
FUNC_SAMPLE func_first_sample,
FUNC_SAMPLE func_next_sample,FUNC_CMP func_cmp,const void* extra)
{
int *L,b,B,B_new,i,*R,neq; /*b for simulation*, neq is for the number of equal signs*/
float* all_P,*all_Q,count;
int ncol=pdata->ncol,nrow=pdata->nrow;
/*allocate the space*/
B=(*func_first_sample)(NULL);
assert(L=(int*)Calloc(ncol,int));
assert(R=(int*)Calloc(nrow,int));
assert(all_P=(float*)Calloc(B,float));
assert(all_Q=(float*)Calloc(B,float));
/*get the original unadjusted p-values first
we'll use the normalized t-statistics*/
get1pvalue(pdata,pdata->L,T,P,func_stat_T,func_first_sample,func_next_sample,func_cmp,extra);
if(myDEBUG)
{
print_farray(stderr,T,pdata->nrow);
print_farray(stderr,P,pdata->nrow);
}
/*sort the test_stat*/
order_mult_data(R,nrow,2,P,cmp_low,T,func_cmp);
/*order_data(P,R,nrow,func_cmp);*/
/*rearrange the data according the unadjusted p-values*/
sort_gene_data(pdata,R);
sort_vector(T,R,nrow);
sort_vector(P,R,nrow);
/*initialze all_Q[]=NA_FLOAT*/
for(b=0;b<B;b++)
all_Q[b]=NA_FLOAT;
/*loop for each gene*/
for(i=nrow-1;i>=0;i--){
get_all_samples_P(pdata->d[i],ncol,all_P,pdata->na,
func_stat,func_first_sample,func_next_sample,func_cmp,extra);
if(myDEBUG)
print_farray(stderr,all_P,B);
/*update all_Q*/
count=0;
B_new=0;
neq=0;
for(b=0;b<B;b++){
if (all_P[b]==NA_FLOAT) break;/*we don't need care about NA pvlaues*/
if(all_Q[b]>all_P[b])
all_Q[b]=all_P[b];/*update q* by the value p*/
if(all_Q[b]==NA_FLOAT) continue;/*skip NA q*/
if(all_Q[b]<P[i]){
count+=1;
}else if (all_Q[b]<=P[i]+EPSILON)/*it'd already > */
neq++;
B_new++;
}
if(myDEBUG)
{
print_farray(stderr,all_Q,B);
fprintf(stderr,"P[%d]=%5.3f,count=%5.2f,neq=%d\n",i,P[i],count,neq);
}
/*assign the Adj_P and Adj_Lower for gene i */
if(B_new!=0) {
Adj_P[i]=(count+neq)/B_new;
if(neq==0)
Adj_Lower[i]=count/B_new;
else Adj_Lower[i]=(count+1)/B_new;
}
else {
Adj_P[i]=NA_FLOAT;
Adj_Lower[i]=NA_FLOAT;
}
/*************************** */
print_b((nrow-i),nrow,"r=");
}
/* to make monotone of Adj_P and Adj_Lower*/
for(i=1;i<nrow;i++)
if(Adj_P[i]<Adj_P[i-1])
Adj_P[i]=Adj_P[i-1];
for(i=1;i<nrow;i++)
if(Adj_Lower[i]<Adj_Lower[i-1])
Adj_Lower[i]=Adj_Lower[i-1];
/*free the spaces*/
Free(L);
Free(R);
Free(all_P);
Free(all_Q);
}
