SEXP getAllFunnels(SEXP Rmpcross)
{
char* stackmem;
{
std::string error;
{
int nFounders;
Rcpp::RObject mpcross_ = Rmpcross;
bool valid = validateMPCross(mpcross_, nFounders, error, true, false, false);
if(!valid)
{
goto signal_error;
}
Rcpp::List mpcross = Rmpcross;
Rcpp::DataFrame pedigree(mpcross["pedigree"]);
Rcpp::IntegerVector id = mpcross["id"];
int nFinals = id.length();
std::vector<int> fid = Rcpp::as<std::vector<int> >(mpcross["fid"]);
Rcpp::IntegerMatrix output(id.length(), nFounders);
std::vector<int> nIntercrossingGenerations;
nIntercrossingGenerations.resize(nFinals, 0);
//get number of intercrossing generations
bool ok = intercrossingGenerations(pedigree, nFounders, id, nIntercrossingGenerations);
if(!ok)
{
error = "Problem determining number of intercrossing generations";
goto signal_error;
}
//now get the actual funnels from the pedigree
int funnel[16];
for(int i = 0; i < id.length(); i++)
{
ok = getFunnel(id[i], pedigree, fid, nIntercrossingGenerations[i], funnel, pedigree.nrows(), nFounders);
if(!ok)
{
std::stringstream ss;
ss << "Problem with pedigree, for individual number " << (i+1) << ", having id " << id[i];
error = ss.str();
goto signal_error;
}
for(int j = 0; j < nFounders; j++) output(i, j) = funnel[j];
}
return output;
}
signal_error:
stackmem = (char*)alloca(error.size() + 4);
memset(stackmem, 0, error.size() + 4);
memcpy(stackmem, error.c_str(), error.size());
}
Rf_error(stackmem);
return R_NilValue;
}
/* This function specifically checks whether the observed data is consistent with the *pedigree*. It assumes that every observed value in the finals is already valid - That is, every observed value contained in the finals is also listed as a possibility in the hetData object
*/
void estimateRFCheckFunnels(Rcpp::IntegerMatrix finals, Rcpp::IntegerMatrix founders, Rcpp::List hetData, Rcpp::S4 pedigree, std::vector<int>& intercrossingGenerations, std::vector<std::string>& warnings, std::vector<std::string>& errors, std::vector<funnelType>& allFunnels, std::vector<funnelType>& lineFunnels)
{
Rcpp::CharacterVector pedigreeLineNames = Rcpp::as<Rcpp::CharacterVector>(pedigree.slot("lineNames"));
//We make a copy of the pedigree line names and sort it (otherwise the std::find relating to pedigreeLineNames is prohibitive)
std::vector<pedigreeLineStruct> sortedLineNames;
sortPedigreeLineNames(pedigreeLineNames, sortedLineNames);
Rcpp::IntegerVector mother = Rcpp::as<Rcpp::IntegerVector>(pedigree.slot("mother"));
Rcpp::IntegerVector father = Rcpp::as<Rcpp::IntegerVector>(pedigree.slot("father"));
bool warnImproperFunnels = Rcpp::as<bool>(pedigree.slot("warnImproperFunnels"));
Rcpp::CharacterVector finalNames = Rcpp::as<Rcpp::CharacterVector>(Rcpp::as<Rcpp::List>(finals.attr("dimnames"))[0]);
Rcpp::CharacterVector markerNames = Rcpp::as<Rcpp::CharacterVector>(Rcpp::as<Rcpp::List>(finals.attr("dimnames"))[1]);
int nFinals = finals.nrow(), nFounders = founders.nrow(), nMarkers = finals.ncol();
if(nFounders != 2 && nFounders != 4 && nFounders != 8 && nFounders != 16)
{
throw std::runtime_error("Number of founders must be 2, 4, 8, or 16");
}
xMajorMatrix<int> foundersToMarkerAlleles(nFounders, nFounders, nMarkers, -1);
for(int markerCounter = 0; markerCounter < nMarkers; markerCounter++)
{
Rcpp::IntegerMatrix currentMarkerHetData = hetData(markerCounter);
for(int founderCounter1 = 0; founderCounter1 < nFounders; founderCounter1++)
{
for(int founderCounter2 = 0; founderCounter2 < nFounders; founderCounter2++)
{
int markerAllele1 = founders(founderCounter1, markerCounter);
int markerAllele2 = founders(founderCounter2, markerCounter);
for(int hetDataRowCounter = 0; hetDataRowCounter < currentMarkerHetData.nrow(); hetDataRowCounter++)
{
if(markerAllele1 == currentMarkerHetData(hetDataRowCounter, 0) && markerAllele2 == currentMarkerHetData(hetDataRowCounter, 1))
{
foundersToMarkerAlleles(founderCounter1, founderCounter2, markerCounter) = currentMarkerHetData(hetDataRowCounter, 2);
}
}
}
}
}
std::vector<long> individualsToCheckFunnels;
for(long finalCounter = 0; finalCounter < nFinals; finalCounter++)
{
individualsToCheckFunnels.clear();
std::string currentLineName = Rcpp::as<std::string>(finalNames(finalCounter));
std::vector<pedigreeLineStruct>::iterator findLineName = std::lower_bound(sortedLineNames.begin(), sortedLineNames.end(), pedigreeLineStruct(currentLineName, -1));
if(findLineName == sortedLineNames.end() || findLineName->lineName != currentLineName)
{
std::stringstream ss;
ss << "Unable to find line number " << finalCounter << " named " << finalNames(finalCounter) << " in pedigree";
throw std::runtime_error(ss.str().c_str());
}
int pedigreeRow = findLineName->index;
//This vector lists all the founders that are ancestors of the current line. This may comprise any number - E.g. if we have an AIC line descended from funnels 1,2,1,2 and 2,3,2,3 then this vector is going it contain 1,2,3
std::vector<int> representedFounders;
if(intercrossingGenerations[finalCounter] == 0)
{
individualsToCheckFunnels.push_back(pedigreeRow);
}
else
{
try
{
getAICParentLines(mother, father, pedigreeRow, intercrossingGenerations[finalCounter], individualsToCheckFunnels);
}
catch(...)
{
std::stringstream ss;
ss << "Error while attempting to trace intercrossing lines for line " << finalNames(finalCounter);
errors.push_back(ss.str());
goto nextLine;
}
}
//Now we know the lines for which we need to check the funnels from the pedigree (note: We don't necessarily have genotype data for all of these, it's purely a pedigree check)
//Fixed length arrays to store funnels. If we have less than 16 founders then part of this is garbage and we don't use that bit....
funnelType funnel, copiedFunnel;
for(std::vector<long>::iterator i = individualsToCheckFunnels.begin(); i != individualsToCheckFunnels.end(); i++)
{
try
{
getFunnel(*i, mother, father, &(funnel.val[0]), nFounders);
}
catch(...)
{
std::stringstream ss;
ss << "Attempting to trace pedigree for line " << finalNames(finalCounter) << ": Unable to get funnel for line " << pedigreeLineNames(*i);
errors.push_back(ss.str());
goto nextLine;
}
//insert these founders into the vector containing all the represented founders
representedFounders.insert(representedFounders.end(), &(funnel.val[0]), &(funnel.val[0]) + nFounders);
//Copy the funnel
memcpy(&copiedFunnel, &funnel, sizeof(funnelType));
std::sort(&(copiedFunnel.val[0]), &(copiedFunnel.val[0]) + nFounders);
if(std::unique(&(copiedFunnel.val[0]), &(copiedFunnel.val[0]) + nFounders) != &(copiedFunnel.val[0]) + nFounders)
{
//If we have intercrossing generations then having repeated founders is an error. Otherwise if warnImproperFunnels is true it's still a warning.
if(intercrossingGenerations[finalCounter] != 0 || warnImproperFunnels)
{
std::stringstream ss;
ss << "Funnel for line " << pedigreeLineNames(*i) << " contained founders {" << funnel.val[0];
if(nFounders == 2)
{
ss << ", " << funnel.val[1] << "}";
}
else if(nFounders == 4)
{
ss << ", " << funnel.val[1] << ", " << funnel.val[2] << ", " << funnel.val[3] << "}";
}
else if(nFounders == 8)
{
ss << ", " << funnel.val[1] << ", " << funnel.val[2] << ", " << funnel.val[3] << ", " << funnel.val[4] << ", " << funnel.val[5] << ", " << funnel.val[6] << ", " << funnel.val[7]<< "}";
}
else if (nFounders == 16)
{
ss << ", " << funnel.val[1] << ", " << funnel.val[2] << ", " << funnel.val[3] << ", " << funnel.val[4] << ", " << funnel.val[5] << ", " << funnel.val[6] << ", " << funnel.val[7] << ", " << funnel.val[8] << ", " << funnel.val[9] << ", " << funnel.val[10] << ", " << funnel.val[11] << ", " << funnel.val[12] << ", " << funnel.val[13] << ", " << funnel.val[14] << ", " << funnel.val[15] << "}";
}
//In this case it's an error
if(intercrossingGenerations[finalCounter] != 0)
{
ss << ". Repeated founders are only allowed with zero generations of intercrossing";
errors.push_back(ss.str());
}
//But if we have zero intercrossing generations then it's only a warning
else
{
ss << ". Did you intend to use all " << nFounders << " founders?";
warnings.push_back(ss.str());
}
}
}
allFunnels.push_back(funnel);
}
//remove duplicates in representedFounders
std::sort(representedFounders.begin(), representedFounders.end());
representedFounders.erase(std::unique(representedFounders.begin(), representedFounders.end()), representedFounders.end());
//Try and check for inconsistent generations of selfing
for(std::vector<int>::iterator i = representedFounders.begin(); i != representedFounders.end(); i++)
{
if(*i > nFounders)
{
std::stringstream ss;
ss << "Error in pedigree for line number " << finalCounter << " named " << finalNames(finalCounter) << ". Inconsistent number of generations of intercrossing";
errors.push_back(ss.str());
goto nextLine;
}
}
//Not having all the founders in the input funnels is more serious if it causes the observed marker data to be impossible. So check for this.
for(int markerCounter = 0; markerCounter < nMarkers; markerCounter++)
{
bool okMarker = false;
//If observed value is an NA then than's ok, continue
int value = finals(finalCounter, markerCounter);
if(value == NA_INTEGER) continue;
for(std::vector<int>::iterator founderIterator1 = representedFounders.begin(); founderIterator1 != representedFounders.end(); founderIterator1++)
{
for(std::vector<int>::iterator founderIterator2 = representedFounders.begin(); founderIterator2 != representedFounders.end(); founderIterator2++)
{
//Note that founderIterator comes from representedFounders, which comes from getFunnel - Which returns values starting at 1, not 0. So we have to subtract one.
if(finals(finalCounter, markerCounter) == foundersToMarkerAlleles((*founderIterator1)-1, (*founderIterator2)-1, markerCounter))
{
okMarker = true;
break;
}
}
}
if(!okMarker)
{
std::stringstream ss;
ss << "Data for marker " << markerNames(markerCounter) << " is impossible for individual " << finalNames(finalCounter) << " with given pedigree";
errors.push_back(ss.str());
if(errors.size() > 1000) return;
goto nextLine;
}
}
//In this case individualsToCheckFunnels contains one element => getFunnel was only called once => we can reuse the funnel variable
if(intercrossingGenerations[finalCounter] == 0)
{
orderFunnel(&(funnel.val[0]), nFounders);
lineFunnels.push_back(funnel);
}
else
{
//Add a dummy value in lineFunnel
for(int i = 0; i < 16; i++) funnel.val[i] = 0;
lineFunnels.push_back(funnel);
}
nextLine:
;
}
}
