fix: fix coercion method from XcmsExperiment to XCMSnExp

sneumann · Aug 5, 2024 · 1bd6d3d · 1bd6d3d
1 parent d0c71d0
commit 1bd6d3d
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/R/XcmsExperiment-functions.R b/R/XcmsExperiment-functions.R
@@ -1168,8 +1168,8 @@ XcmsExperiment <- function() {
  files = fileNames(from),
  smoothed = NA)
  n@phenoData <- new("NAnnotatedDataFrame", as.data.frame(sampleData(from)))
- fd <- as.data.frame(spectra(from)@backend@spectraData)
- fd$fileIdx <- match(fd$dataStorage, fileNames(from))
+ fd <- as.data.frame(MsExperiment::spectra(from)@backend@spectraData)
+ fd$fileIdx <- match(fd$dataStorage, unique(fd$dataStorage))
  fd <- fd[, !colnames(fd) %in% c("dataStorage", "dataOrigin")]
  colnames(fd) <- sub("scanIndex", "spIdx", colnames(fd))
  colnames(fd) <- sub("rtime", "retentionTime", colnames(fd))

diff --git a/tests/testthat/test_XcmsExperiment-functions.R b/tests/testthat/test_XcmsExperiment-functions.R
@@ -210,7 +210,7 @@ test_that(".xcms_experiment_to_xcms_n_exp works", {
 
  a <- loadXcmsData("xmse")
  a1 <- a[1]
- a1@spectra <- Spectra::setBackend(spectra(a1), MsBackendMemory())
+ a1@spectra <- Spectra::setBackend(spectra(a1), Spectra::MsBackendMemory())
  expect_error(xcms:::.xcms_experiment_to_xcms_n_exp(a1), "MsBackendMzR")
 
  res <- xcms:::.xcms_experiment_to_xcms_n_exp(a)