Import methods

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.1
+Version: 4.3.2
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
@@ -60,10 +60,10 @@ Imports:
     S4Vectors,
     IRanges,
     SummarizedExperiment,
-    MsCoreUtils (>= 1.15.5),
+    MsCoreUtils (>= 1.15.7),
     MsFeatures,
     MsExperiment (>= 1.5.4),
-    Spectra (>= 1.13.7),
+    Spectra (>= 1.15.3),
     progress,
     jsonlite,
     RColorBrewer,

NAMESPACE

@@ -33,7 +33,7 @@ importFrom("SummarizedExperiment", "rowData")
 importFrom("SummarizedExperiment", "rowData<-")
 importFrom("SummarizedExperiment", "assay")
 importFrom("MsCoreUtils", "rbindFill", "closest", "i2index", "sumi", "between",
-           "maxi", "breaks_ppm", "force_sorted")
+           "maxi", "breaks_ppm", "force_sorted", "common_path")
 importFrom("RColorBrewer", "brewer.pal")
 
 importFrom("graphics", "image", "boxplot", "matplot", "rect", "axis",
@@ -52,7 +52,7 @@ importFrom("stats", "aov", "approx", "convolve", "cor", "deriv3",
            "rnorm", "runif", "dbeta", "resid")
 importFrom("utils", "flush.console", "head", "object.size",
            "packageVersion", "read.csv", "tail", "write.csv",
-           "write.table", "capture.output", "data")
+           "write.table", "capture.output", "data", "read.table")
 
 importFrom("MassSpecWavelet", "peakDetectionCWT", "tuneInPeakInfo")
 
@@ -254,7 +254,8 @@ export(
     "loadXcmsData",
     "matchLamasChromPeaks",
     "summarizeLamaMatch",
-    "matchedRtimes"
+    "matchedRtimes",
+    "XcmsExperiment"
 )
 
 ## New analysis methods
@@ -558,15 +559,17 @@ importMethodsFrom("Spectra", "uniqueMsLevels")
 importMethodsFrom("Spectra", "selectSpectraVariables")
 importMethodsFrom("Spectra", "setBackend")
 importMethodsFrom("Spectra", "dataOrigin")
-importMethodsFrom("Spectra", "dataStorage")
+importMethodsFrom("Spectra", "dataStorage", "dataStorage<-")
 importMethodsFrom("Spectra", "spectraVariables")
 importMethodsFrom("Spectra", "rtime<-")
 importMethodsFrom("Spectra", "ionCount")
 importMethodsFrom("Spectra", "precursorMz")
 importMethodsFrom("Spectra", "$")
 importMethodsFrom("Spectra", "uniqueMsLevels")
 importMethodsFrom("Spectra", "backendBpparam")
-importFrom("Spectra", "MsBackendMemory")
+importFrom("Spectra", "MsBackendMemory", "dataStorageBasePath",
+           "dataStorageBasePath<-", "processingChunkSize",
+           "dropNaSpectraVariables", "MsBackendMzR", "filterEmptySpectra")
 
 ## MsExperiment things
 importClassesFrom("MsExperiment", "MsExperiment")
@@ -590,12 +593,15 @@ exportMethods("filterMzRange")
 exportMethods("fromFile")
 exportMethods("fileNames")
 
-## saving xcms objects things
+## saving/loading xcms objects things
 importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
            "read_json")
+importFrom("stats", "setNames")
+importFrom("MsCoreUtils", "between")
 export("RDataParam")
 export("PlainTextParam")
-exportMethods("storeResults")
+exportMethods("storeResults", "loadResults")
+
 
 ## filtering features things
 importFrom("MetaboCoreUtils", "rowRsd", "rowDratio", "rowPercentMissing",

NEWS.md

@@ -1,5 +1,10 @@
 # xcms 4.3
 
+## Changes in version 4.3.2
+
+- Addition of generic function `loadResults()`and method for import using 
+  `RDataParam` and `PlaintTextParam`.
+
 ## Changes in version 4.3.1
 
 - Support excluding samples or sample groups from defining features with
@@ -8,7 +13,6 @@
 - Fix in `dropFeatureDefinitions()` that was not correctly removing additional
   metadata from gap-filled chromatographic peaks.
 
-
 # xcms 4.1
 
 ## Changes in version 4.1.14

R/AllGenerics.R

@@ -1486,6 +1486,66 @@ setGeneric("kNN<-", function(object, value) standardGeneric("kNN<-"))
 
 ## L
 setGeneric("levelplot", function(x, data, ...) standardGeneric("levelplot"))
+#' @title Import various file format as XcmsExperiment object
+#'
+#' @description
+#'
+#' The `loadResults` function allows to import and create an `XcmsExperiment`
+#' object from a file. Multiple formats for importing are available and can be
+#' defined by the `param` argument.
+#'
+#' Supported `param` objects are:
+#'
+#' - [`RDataParam`]: Import an `MsExperiment` or `XcmsExperiment` object from
+#'   an .RData file.
+#'
+#' - [`PlainTextParam`]: Import an `MsExperiment` or `XcmsExperiment` object
+#'   from a folder of text files.
+#'
+#' - `MzTabParam`: Load a MzTab-m file (to be defined).
+#'
+#' For specific examples, see the help pages of the individual parameter classes
+#' listed above.
+#'
+#' @param object Define the class of the object to be imported. It can be one
+#' of the following classes: [`XcmsExperiment()`], [`MsExperiment()`] for now,
+#' more class will be supported in the future.
+#'
+#' @param param The parameter object selecting and configuring the format for
+#' saving. It can be one of the following classes: [`RDataParam`],
+#' [`PlainTextParam`], or `MzTabParam`.
+#'
+#' @param ... Optional parameters.
+#'
+#' @note
+#' The same `param` object can be used to import as it was used for export with
+#' the `storeResults()` function.
+#'
+#' @name loadResults
+#'
+#' @author Philippine Louail
+#'
+#' @examples
+#' ## Load a test data set with detected peaks
+#' faahko_sub <- loadXcmsData("faahko_sub2")
+#'
+#' ## Save as RData
+#' param <- RDataParam(fileName = "example_xcms_object")
+#' storeResults(object = faahko_sub, param = param)
+#'
+#' ## Load this saved dataset
+#' xcmse <- loadResults(object = XcmsExperiment(),param = param)
+#'
+#' ## Save as a collection of plain text files
+#' pth = file.path(tempdir(), "test")
+#' param <- PlainTextParam(path = pth)
+#' storeResults(object = faahko_sub, param = param)
+#'
+#' ## Load this saved dataset
+#' faahko_load <- loadResults(object= XcmsExperiment(), param = param)
+#'
+#' @md
+setGeneric("loadResults", function(object, param,...) standardGeneric("loadResults"))
 setGeneric("localAlignment", function(object) standardGeneric("localAlignment"))
 setGeneric("localAlignment<-", function(object, value) standardGeneric("localAlignment<-"))
 setGeneric("loadRaw", function(object, ...) standardGeneric("loadRaw"))