refactor: import filterSpectra from MsExperiment

- Import `filterSpectra` from `MsExperiment`.

.github/workflows/check-bioc.yml

@@ -203,6 +203,7 @@ jobs:
           BiocManager::install("MsBackendMgf")
           BiocManager::install("MetaboCoreUtils")
           BiocManager::install("magick")
+          BiocManager::install("RforMassSpectrometry/MsExperiment")
 
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))

DESCRIPTION

@@ -58,7 +58,7 @@ Imports:
     SummarizedExperiment,
     MsCoreUtils (>= 1.15.3),
     MsFeatures,
-    MsExperiment (>= 1.5.3),
+    MsExperiment (>= 1.5.4),
     Spectra (>= 1.13.2),
     progress,
     multtest,

NAMESPACE

@@ -572,6 +572,7 @@ importFrom("Spectra", "MsBackendMemory")
 ## MsExperiment things
 importClassesFrom("MsExperiment", "MsExperiment")
 importMethodsFrom("MsExperiment", "spectra")
+importMethodsFrom("MsExperiment", "filterSpectra")
 importMethodsFrom("BiocGenerics", "do.call")
 importMethodsFrom("BiocGenerics", "rbind")
 importFrom("MsExperiment", "MsExperiment")

R/MsExperiment-functions.R

@@ -247,37 +247,6 @@
         USE.NAMES = FALSE, BPPARAM = BPPARAM)
 }
 
-#' generic method to apply a filtering to the spectra data. The function will
-#' apply the filtering and (most importantly) keep/update the link between
-#' spectra and samples.
-#'
-#' @importMethodsFrom Spectra selectSpectraVariables
-#'
-#' @param x `MsExperiment`.
-#'
-#' @param FUN filter function.
-#'
-#' @param ... parameters for `FUN`.
-#'
-#' @author Johannes Rainer
-#'
-#' @noRd
-.mse_filter_spectra <- function(x, FUN, ...) {
-    ls <- length(spectra(x))
-    have_links <- length(x@sampleDataLinks[["spectra"]]) > 0
-    if (have_links)
-        x@spectra$._SPECTRA_IDX <- seq_len(ls)
-    x@spectra <- FUN(x@spectra, ...)
-    if (have_links) {
-        if (ls != length(spectra(x)))
-            x <- .update_sample_data_links_spectra(x)
-        svs <- unique(c(spectraVariables(spectra(x)), "mz", "intensity"))
-        x@spectra <- selectSpectraVariables(
-            x@spectra, svs[svs != "._SPECTRA_IDX"])
-    }
-    x
-}
-
 #' Ensure that each spectrum is assigned to a sample and that we only have 1:1
 #' mappings. That is important for most code involving splitting of samples
 #' etc.

R/MsExperiment.R

@@ -2,8 +2,7 @@
 setMethod("filterRt", "MsExperiment",
           function(object, rt = numeric(), ...) {
               message("Filter spectra")
-              object <- .mse_filter_spectra(object, filterRt, rt = rt, ...)
-              object
+              filterSpectra(object, filterRt, rt = rt, ...)
           })
 
 #' @rdname XcmsExperiment
@@ -24,8 +23,7 @@ setMethod("filterMz", "MsExperiment",
 setMethod("filterMsLevel", "MsExperiment",
           function(object, msLevel. = uniqueMsLevels(object)) {
               message("Filter spectra")
-              .mse_filter_spectra(object, filterMsLevel,
-                                  msLevel. = msLevel.)
+              filterSpectra(object, filterMsLevel, msLevel. = msLevel.)
           })
 
 #' @rdname XcmsExperiment
@@ -93,7 +91,7 @@ setMethod("polarity", "MsExperiment", function(object) {
 #' @rdname XcmsExperiment
 setMethod(
     "filterIsolationWindow", "MsExperiment", function(object, mz = numeric()) {
-        .mse_filter_spectra(object, filterIsolationWindow, mz = mz)
+        filterSpectra(object, filterIsolationWindow, mz = mz)
     })
 
 #' @rdname XcmsExperiment

R/XcmsExperiment.R

@@ -777,7 +777,7 @@ setMethod(
     function(object, mz = numeric()) {
         if (length(mz) > 1L)
             mz <- mz[1L]
-        object <- .mse_filter_spectra(object, filterIsolationWindow, mz = mz)
+        object <- filterSpectra(object, filterIsolationWindow, mz = mz)
         if (hasChromPeaks(object) && length(mz) &&
             all(c("isolationWindowLowerMz", "isolationWindowUpperMz") %in%
                 colnames(object@chromPeakData))) {

tests/testthat/test_MsExperiment-functions.R

@@ -141,42 +141,6 @@ test_that(".mse_find_chrom_peaks_chunk works", {
     expect_true(is.null(res[[2L]]))
 })
 
-test_that(".mse_filter_spectra works", {
-    ## Create a custom, small test object.
-    fls <- normalizePath(faahko_3_files)
-    df <- data.frame(mzML_file = basename(fls),
-                     dataOrigin = fls,
-                     sample = c("ko15", "ko16", "ko18"))
-    a <- Spectra::Spectra(fls[1])
-    b <- Spectra::Spectra(fls[2])
-    c <- Spectra::Spectra(fls[3])
-
-    ## Select first 10 spectra from a and c and last 10 from b and combine them
-    sps <- c(a[1:10], b[(length(b)-9):length(b)], c[1:10])
-
-    tst <- MsExperiment()
-    spectra(tst) <- sps
-    sampleData(tst) <- DataFrame(df)
-    ## Link samples to spectra.
-    tst <- linkSampleData(tst, with = "sampleData.dataOrigin = spectra.dataOrigin")
-
-    res <- .mse_filter_spectra(tst, filterRt, rt = c(2502, 2505))
-    expect_true(length(spectra(res)) == 4L)
-    expect_equal(res@sampleDataLinks[["spectra"]],
-                 cbind(c(1L, 1L, 3L, 3L), 1:4))
-
-    ## Some artificial sample assignment.
-    tst@sampleDataLinks[["spectra"]] <- cbind(
-        c(1, 1, 1, 2, 2, 2, 3, 3, 3),
-        c(2, 3, 4, 2, 3, 4, 2, 3, 4))
-    res <- .mse_filter_spectra(tst, filterRt, rt = c(2502, 2505))
-    ## Filtering will filter based on rt
-    expect_true(length(spectra(res)) == 4L)
-    ## Sample assignment should map the first 2 spectra to all 3 samples
-    expect_equal(res@sampleDataLinks[["spectra"]],
-                 cbind(c(1L, 1L, 2L, 2L, 3L, 3L), c(1L, 2L, 1L, 2L, 1L, 2L)))
-})
-
 test_that(".mse_check_spectra_sample_mapping works", {
     expect_true(length(.mse_check_spectra_sample_mapping(mse)) == 0)