//[[Rcpp::export]]
DataFrame reldist_impl(GroupedDataFrame x, GroupedDataFrame y) {
std::vector<float> rel_distances ;
std::vector<int> indices_x ;
DataFrame df_x = x.data() ;
PairedGroupApply(x, y, reldist_grouped, std::ref(indices_x), std::ref(rel_distances));
DataFrame subset_x = DataFrameSubsetVisitors(df_x, names(df_x)).subset(indices_x, "data.frame");
auto ncol_x = subset_x.size() ;
CharacterVector names(ncol_x + 1) ;
CharacterVector names_x = subset_x.attr("names") ;
List out(ncol_x + 1) ;
// x names, data
for( int i=0; i<ncol_x; i++) {
names[i] = names_x[i] ;
out[i] = subset_x[i] ;
}
out[ncol_x] = rel_distances ;
names[ncol_x] = "reldist" ;
out.attr("names") = names ;
out.attr("class") = classes_not_grouped() ;
auto nrows = subset_x.nrows() ;
set_rownames(out, nrows) ;
return out ;
}
//[[Rcpp::export]]
DataFrame intersect_impl(GroupedDataFrame x, GroupedDataFrame y,
const std::string& suffix_x = ".x",
const std::string& suffix_y = ".y") {
// indices for subsetting
std::vector<int> indices_x ;
std::vector<int> indices_y ;
// overlap sizes
std::vector<int> overlap_sizes ;
auto data_x = x.data() ;
auto data_y = y.data() ;
// set up interval trees for each chromosome and apply intersect_group
GroupApply(x, y, intersect_group, std::ref(indices_x), std::ref(indices_y), std::ref(overlap_sizes));
DataFrame subset_x = DataFrameSubsetVisitors(data_x, names(data_x)).subset(indices_x, "data.frame");
DataFrame subset_y = DataFrameSubsetVisitors(data_y, names(data_y)).subset(indices_y, "data.frame");
auto ncol_x = subset_x.size() ;
auto ncol_y = subset_y.size() ;
CharacterVector names(ncol_x + ncol_y) ;
CharacterVector names_x = subset_x.attr("names") ;
CharacterVector names_y = subset_y.attr("names") ;
// replacing y chrom with overlap, same number of cols
List out(ncol_x + ncol_y) ;
// x names, data
for (int i = 0; i < ncol_x; i++) {
auto name_x = as<std::string>(names_x[i]) ;
if (name_x != "chrom") {
name_x += suffix_x ;
}
names[i] = name_x ;
out[i] = subset_x[i] ;
}
// y names, data
for (int i = 0; i < ncol_y; i++) {
auto name_y = as<std::string>(names_y[i]) ;
if (name_y == "chrom") continue ;
name_y += suffix_y ;
names[i + ncol_x - 1] = name_y ;
out[i + ncol_x - 1] = subset_y[i] ;
}
// overlaps
out[ncol_x + ncol_y - 1] = overlap_sizes ;
names[ncol_x + ncol_y - 1] = ".overlap" ;
out.attr("names") = names ;
out.attr("class") = classes_not_grouped() ;
auto nrows = subset_x.nrows() ;
set_rownames(out, nrows) ;
return out ;
}
//[[Rcpp::export]]
DataFrame flank_impl(DataFrame inputTable, DataFrame genome,
double both = 0, double left = 0, double right = 0,
bool fraction = false, bool strand = false, bool trim = false) {
// Warnings
if (both == 0 & left == 0 & right == 0)
stop("specify one of both, left, right");
if (both != 0 & (left != 0 || right != 0))
stop("ambiguous side spec for bed_flank");
std::vector<std::string> TableNames = inputTable.names();
int TableLen = TableNames.size();
bool strandTest = false;
for (int i = 0; i < TableLen; i++)
if (TableNames[i] == "strand")
strandTest = true;
if (strand == true & strandTest == false)
stop("expected strand column");
// Set both
if (both > 0) left = right = both;
// Set input and output vectors
std::vector<std::string> chroms = inputTable["chrom"];
std::vector<int> startCoords = inputTable["start"];
std::vector<int> endCoords = inputTable["end"];
int N = startCoords.size();
std::vector<int> coordSize(N);
std::vector<int> idxOut;
std::vector<double> startOut;
std::vector<double> endOut;
// Create unordered map for chrom sizes
genome_map_t chroMap = makeChromSizes(genome);
for (int i = 0; i < N; i++) {
int leftstart;
int leftend;
int rightstart;
int rightend;
// strand
if (strand == true) {
std::vector<std::string> strands = inputTable["strand"];
// strand, fraction
if (fraction == true) {
coordSize[i] = endCoords[i] - startCoords[i];
if (strands[i] == "+") {
leftstart = startCoords[i] - coordSize[i] * left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + coordSize[i] * right;
} else {
leftstart = endCoords[i];
leftend = endCoords[i] + coordSize[i] * left;
rightstart = startCoords[i] - coordSize[i] * right;
rightend = startCoords[i];
}
// strand, no fraction
} else {
if (strands[i] == "+") {
leftstart = startCoords[i] - left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + right;
} else {
leftstart = endCoords[i];
leftend = endCoords[i] + left;
rightstart = startCoords[i] - right;
rightend = startCoords[i];
}
}
// no strand
} else {
// no strand, fraction
if (fraction == true) {
coordSize[i] = endCoords[i] - startCoords[i];
leftstart = startCoords[i] - coordSize[i] * left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + coordSize[i] * right;
// no strand, no fraction
} else {
leftstart = startCoords[i] - left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + right;
}
}
// Compare new intervals to chrom sizes
std::string chrom = chroms[i];
int chrSize = chroMap[chrom];
if (left > 0 & leftstart > 0 & leftend <= chrSize) {
startOut.push_back (leftstart);
endOut.push_back (leftend);
idxOut.push_back (i);
} else if (trim == true & leftstart > 0 & leftend > chrSize) {
startOut.push_back (leftstart);
endOut.push_back (chrSize);
idxOut.push_back (i);
} else if (trim == true & leftstart <= 0 & leftend <= chrSize) {
startOut.push_back (1);
endOut.push_back (leftend);
idxOut.push_back (i);
} else if (trim == true & leftstart <= 0 & leftend > chrSize) {
startOut.push_back (1);
endOut.push_back (chrSize);
idxOut.push_back (i);
}
if (right > 0 & rightstart > 0 & rightend <= chrSize) {
startOut.push_back (rightstart);
endOut.push_back (rightend);
idxOut.push_back (i);
} else if (trim == true & rightstart > 0 & rightend > chrSize) {
startOut.push_back (rightstart);
endOut.push_back (chrSize);
idxOut.push_back (i);
} else if (trim == true & rightstart <= 0 & rightend <= chrSize) {
startOut.push_back (1);
endOut.push_back (rightend);
idxOut.push_back (i);
} else if (trim == true & rightstart <= 0 & rightend > chrSize) {
startOut.push_back (1);
endOut.push_back (chrSize);
idxOut.push_back (i);
}
}
// Write new DataFrame
DataFrame outTable = DataFrameSubsetVisitors(inputTable, names(inputTable)).subset(idxOut, "data.frame");
outTable["start"] = startOut;
outTable["end"] = endOut;
return outTable;
}
