refactor: add parameter f to more functions

rformassspectrometry · Nov 24, 2023 · 0e555dc · 0e555dc
1 parent 194f104
commit 0e555dc
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Showing 3 changed files with 27 additions and 13 deletions.
diff --git a/R/Spectra.R b/R/Spectra.R
@@ -827,6 +827,8 @@ NULL
 #'     splitted. For `filterPrecursorScan`:
 #'     defining which spectra belong to the same original data file (sample).
 #'     Defaults to `f = dataOrigin(x)`.
+#'     For `intensity`, `mz` and `peaksData`: factor defining how data should
+#'     be chunk-wise loaded an processed. Defaults to [processingChunkFactor()].
 #'
 #' @param FUN For `addProcessing`: function to be applied to the peak matrix
 #'     of each spectrum in `object`. For `compareSpectra`: function to compare
@@ -1630,8 +1632,8 @@ setMethod("acquisitionNum", "Spectra", function(object)
 #' @rdname Spectra
 setMethod(
     "peaksData", "Spectra",
-    function(object, columns = c("mz", "intensity"), ..., BPPARAM = bpparam()) {
-        f <- .parallel_processing_factor(object)
+    function(object, columns = c("mz", "intensity"),
+             f = processingChunkFactor(object), ..., BPPARAM = bpparam()) {
         if (length(object@processingQueue) || length(f))
             SimpleList(.peaksapply(object, columns = columns, f = f))
         else SimpleList(peaksData(object@backend, columns = columns))
@@ -1692,8 +1694,9 @@ setMethod("dropNaSpectraVariables", "Spectra", function(object) {
 })
 
 #' @rdname Spectra
-setMethod("intensity", "Spectra", function(object, ...) {
-    f <- .parallel_processing_factor(object)
+setMethod("intensity", "Spectra", function(object,
+                                           f = processingChunkFactor(object),
+                                           ...) {
     if (length(object@processingQueue) || length(f))
         NumericList(.peaksapply(object, FUN = function(z, ...) z[, 2],
                                 f = f, ...), compress = FALSE)
@@ -1835,8 +1838,8 @@ setMethod("length", "Spectra", function(x) length(x@backend))
 setMethod("msLevel", "Spectra", function(object) msLevel(object@backend))
 
 #' @rdname Spectra
-setMethod("mz", "Spectra", function(object, ...) {
-    f <- .parallel_processing_factor(object)
+setMethod("mz", "Spectra", function(object, f = processingChunkFactor(object),
+                                    ...) {
     if (length(object@processingQueue) || length(f))
         NumericList(.peaksapply(object, FUN = function(z, ...) z[, 1],
                                 f = f, ...), compress = FALSE)

diff --git a/man/Spectra.Rd b/man/Spectra.Rd
diff --git a/vignettes/Spectra-large-scale.Rmd b/vignettes/Spectra-large-scale.Rmd
@@ -215,6 +215,12 @@ chunk-wise) processing. These functions are:
 - `estimatePrecursorIntensity`: parameter `f` (defaults to `dataOrigin(x)`)
   defines the splitting and processing. This should represent the original data
   files the spectra data derives from.
+- `intensity`: parameter `f` (defaults to `processingChunkFactor(object)`)
+  defines if and how the data should be split for parallel processing.
+- `mz`: parameter `f` (defaults to `processingChunkFactor(object)`)
+  defines if and how the data should be split for parallel processing.
+- `peaksData`: parameter `f` (defaults to `processingChunkFactor(object)`)
+  defines if and how the data should be split for parallel processing.
 - `setBackend`: parameter `f` (defaults to `processingChunkFactor(object)`)
   defines if and how the data should be split for parallel processing.
 
@@ -223,12 +229,9 @@ on the `processingChunkFactor`:
 
 - `containsMz`.
 - `containsNeutralLoss`.
-- `intensity`.
 - `ionCount`.
 - `isCentroided`.
 - `isEmpty`.
-- `mz`.
-- `peaksData`.