void mqmscan(int Nind, int Nmark,int Npheno,int **Geno,int **Chromo, double **Dist, double **Pheno, int **Cofactors, int Backwards, int RMLorML,double Alfa,
int Emiter, double Windowsize,double Steps, double Stepmi,double Stepma,int NRUN,int out_Naug,int **INDlist, double **QTL, int re_estimate,
RqtlCrossType rqtlcrosstype,int domi,int verbose){
int cof_cnt=0;
MQMMarkerMatrix markers = newMQMMarkerMatrix(Nmark+1,Nind);
cvector cofactor = newcvector(Nmark);
vector mapdistance = newvector(Nmark);
MQMCrossType crosstype = determine_MQMCross(Nmark,Nind,(const int **)Geno,rqtlcrosstype);
change_coding(&Nmark, &Nind, Geno, markers, crosstype); // Change all the markers from R/qtl format to MQM internal
for (int i=0; i< Nmark; i++) {
mapdistance[i] = POSITIONUNKNOWN; // Mapdistances
mapdistance[i] = Dist[0][i];
cofactor[i] = MNOCOF; // Cofactors
if (Cofactors[0][i] == 1) {
cofactor[i] = MCOF; // Set cofactor
cof_cnt++;
}
if (Cofactors[0][i] == 2) {
cofactor[i] = MSEX;
cof_cnt++;
}
if (cof_cnt+10 > Nind){ fatal("Setting %d cofactors would leave less than 10 degrees of freedom.\n", cof_cnt); }
}
char reestimate = 'y';
if(re_estimate == 0) reestimate = 'n';
if (crosstype != CF2) { // Determine what kind of cross we have
if (verbose==1) Rprintf("INFO: Dominance setting ignored (setting dominance to 0)\n"); // Update dominance accordingly
domi = 0;
}
bool dominance=false;
if(domi != 0){ dominance=true; }
//WE HAVE EVERYTHING START WITH MAIN SCANNING FUNCTION
analyseF2(Nind, &Nmark, &cofactor, (MQMMarkerMatrix)markers, Pheno[(Npheno-1)], Backwards, QTL, &mapdistance, Chromo, NRUN, RMLorML, Windowsize,
Steps, Stepmi, Stepma, Alfa, Emiter, out_Naug, INDlist, reestimate, crosstype, dominance, verbose);
if (re_estimate) {
if (verbose==1) Rprintf("INFO: Sending back the re-estimated map used during the MQM analysis\n");
for (int i=0; i< Nmark; i++) {
Dist[0][i] = mapdistance[i];
}
}
if (Backwards) {
if (verbose==1) Rprintf("INFO: Sending back the model\n");
for (int i=0; i< Nmark; i++) { Cofactors[0][i] = cofactor[i]; }
}
if(verbose) Rprintf("INFO: All done in C returning to R\n");
#ifndef STANDALONE
R_CheckUserInterrupt(); /* check for ^C */
R_FlushConsole();
#endif
return;
} /* end of function mqmscan */
void R_mqmaugment(int *geno, double *dist, double *pheno, int *auggeno,
double *augPheno, int *augIND, int *Nind, int *Naug, int *Nmark,
int *Npheno, int *maxind, int *maxiaug, double *minprob, int
*chromo, int *rqtlcrosstypep, int *augment_strategy, int *verbosep) {
int **Geno;
double **Pheno;
double **Dist;
int **NEW; //Holds the output for the augmentdata function
int **Chromo;
double **NEWPheno; //New phenotype vector
int **NEWIND; //New list of individuals
const int nind0 = *Nind; //Individuals we start with
const int verbose = *verbosep;
const RqtlCrossType rqtlcrosstype = (RqtlCrossType) *rqtlcrosstypep;
if(verbose) Rprintf("INFO: Starting C-part of the data augmentation routine\n");
ivector new_ind;
MQMMarkerMatrix markers = newMQMMarkerMatrix(*Nmark, nind0);
vector mapdistance = newvector(*Nmark);
ivector chr = newivector(*Nmark);
//Reorganise the pointers into arrays, Singletons are just cast into the function
reorg_geno(nind0, *Nmark, geno, &Geno);
reorg_int(*Nmark, 1, chromo, &Chromo);
reorg_pheno(nind0, *Npheno, pheno, &Pheno);
reorg_pheno(*Nmark, 1, dist, &Dist);
reorg_int(*maxind, *Nmark, auggeno, &NEW);
reorg_int((*maxiaug)*nind0, 1, augIND, &NEWIND);
reorg_pheno((*maxiaug)*nind0, 1, augPheno, &NEWPheno);
MQMCrossType crosstype = determine_MQMCross(*Nmark, *Nind, (const int **)Geno, rqtlcrosstype); // Determine cross
change_coding(Nmark, Nind, Geno, markers, crosstype); // Change all the markers from R/qtl format to MQM internal
if(verbose) Rprintf("INFO: Filling the chromosome matrix\n");
for (int i=0; i<(*Nmark); i++) {
//Set some general information structures per marker
mapdistance[i] = POSITIONUNKNOWN;
mapdistance[i] = Dist[0][i];
chr[i] = Chromo[0][i];
}
if(mqmaugmentfull(&markers,Nind,Naug,&new_ind,*minprob, *maxind, *maxiaug,&Pheno,*Nmark,chr,mapdistance,*augment_strategy,crosstype,verbose)){
//Data augmentation finished succesfully, encode it back into RQTL format
for (int i = 0; i<(*Nmark); i++) {
for (int j = 0; j<(*Naug); j++) {
//Rprintf("INFO: Phenotype after return: %f",NEWPheno[0][j]);
NEWPheno[0][j] = Pheno[0][j];
NEWIND[0][j] = new_ind[j];
NEW[i][j] = 9;
if (markers[i][j] == MAA) {
NEW[i][j] = 1;
}
if (markers[i][j] == MH) {
NEW[i][j] = 2;
}
if (markers[i][j] == MBB) { // [karl:] this might need to be changed for RIL
crosstype==CRIL ? NEW[i][j]=2 : NEW[i][j] = 3; //[Danny:] This should solve it
}
if (markers[i][j] == MNOTAA) {
NEW[i][j] = 5;
}
if (markers[i][j] == MNOTBB) {
NEW[i][j] = 4;
}
}
}
if (verbose) {
Rprintf("# Unique individuals before augmentation:%d\n", nind0);
Rprintf("# Unique selected individuals:%d\n", *Nind);
Rprintf("# Marker p individual:%d\n", *Nmark);
Rprintf("# Individuals after augmentation:%d\n", *Naug);
Rprintf("INFO: Data augmentation succesfull\n");
}
} else {
//Unsuccessfull data augmentation exit
Rprintf("INFO: This code should not be reached, data corruption could have occured. Please re-run this analysis.\n");
*Naug = nind0;
for (int i=0; i<(*Nmark); i++) {
for (int j=0; j<(*Naug); j++) {
NEWPheno[0][j] = Pheno[0][j];
NEW[i][j] = 9;
if (markers[i][j] == MAA) {
NEW[i][j] = 1;
}
if (markers[i][j] == MH) {
NEW[i][j] = 2;
}
if (markers[i][j] == MBB) { // [Karl:] this might need to be changed for RIL
crosstype==CRIL ? NEW[i][j]=2 : NEW[i][j] = 3; // [Danny:] This should solve it
}
if (markers[i][j] == MNOTAA) {
NEW[i][j] = 5;
}
if (markers[i][j] == MNOTBB) {
NEW[i][j] = 4;
}
}
}
fatal("Data augmentation failed", "");
}
delMQMMarkerMatrix(markers,*Nmark); // [Danny:] This looked suspicious, we were leaking memory here because we didn't clean it
Free(mapdistance);
Free(chr);
return;
}
