Merge pull request #265 from jorainer/master

feat: pwiz returns peak matrices with column names
sneumann · Mar 20, 2022 · 88b1c19 · 88b1c19
2 parents 68e1720 + 0e6e520
commit 88b1c19
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Showing 4 changed files with 10 additions and 1 deletion.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mzR
 Type: Package
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
        (mass spectrometry data)
-Version: 2.29.4
+Version: 2.29.5
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
 Authors@R: c(
     person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),

diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+CHANGES IN VERSION 2.27.5
+-------------------------
+ o `peaks` method for pwiz backend sets colnames on returned matrices.
+
 CHANGES IN VERSION 2.29.4
 -------------------------
  o Re-apply fix for compile error on clang by Kurt Hornik, closes #263

diff --git a/inst/unitTests/test_pwiz.R b/inst/unitTests/test_pwiz.R
@@ -11,6 +11,7 @@ test_mzXML <- function() {
     checkTrue(is.matrix(peaks(mzxml,1)))
     pks <- peaks(mzxml, 2:3)
     checkTrue(length(pks) == 2)
+    checkEquals(colnames(pks[[1L]]), c("mz", "intensity"))
     peaksCount(mzxml)
     hdr <- header(mzxml)
     checkTrue(any(colnames(hdr) == "spectrumId"))
@@ -39,6 +40,7 @@ test_mzML <- function() {
     pks <- peaks(mzml)
     pks <- peaks(mzml,1)
     pks <- peaks(mzml,2:3)
+    checkEquals(colnames(pks[[1L]]), c("mz", "intensity"))
     peaksCount(mzml)
     hdr <- header(mzml)
     checkTrue(any(colnames(hdr) == "spectrumId"))

diff --git a/src/RcppPwiz.cpp b/src/RcppPwiz.cpp
@@ -401,6 +401,7 @@ Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector whichScan) {
     std::vector<double> data;
     Rcpp::NumericVector data_matrix;
     Rcpp::List res(n_want);
+    Rcpp::CharacterVector cn = Rcpp::CharacterVector::create("mz", "intensity");
     for (size_t i = 0; i < n_want; i++) {
       current_scan = whichScan[i];
       if (current_scan < 1 || current_scan > n_scans) {
@@ -414,6 +415,7 @@ Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector whichScan) {
       ints = sp->getIntensityArray();
       if (!mzs.get() || !ints.get()) {
 	Rcpp::NumericMatrix pks(0, 2);
+	Rcpp::colnames(pks) = cn;
 	res[i] = pks;
 	continue;
       }
@@ -423,6 +425,7 @@ Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector whichScan) {
       data.insert(data.end(), ints->data.begin(), ints->data.end());
       data_matrix = Rcpp::wrap(data);
       data_matrix.attr("dim") = Rcpp::Dimension(ints->data.size(), 2);
+      Rcpp::colnames(data_matrix) = cn;
       res[i] = data_matrix;
     }
     return res;