Type metadata

.Rbuildignore

@@ -7,3 +7,5 @@ docs
 ^\.github$
 .editorconfig
 .git
+^doc$
+^Meta$

.github/workflows/check-bioc.yml

@@ -232,9 +232,9 @@ jobs:
       #     cd preprocessCore
       #     R CMD INSTALL --configure-args="--disable-threading"  .
 
-      - name: Manually install latest RforMassSpectrometry/QFeatures
+      - name: Manually install from a branch
         run: |
-          BiocManager::install("RforMassSpectrometry/QFeatures")
+          remotes::install_github("RforMassSpectrometry/QFeatures", ref = "typeMetadata")
         shell: Rscript {0}
 
       - name: Session info

.gitignore

@@ -3,3 +3,6 @@
 *.RData
 .Ruserdata
 *.Rproj
+tests/testthat/_snaps
+/doc/
+/Meta/

NEWS.md

@@ -1,13 +1,29 @@
 # scp 1.17
 
+## scp 1.17.0
+
+- New Bioconductor 3.21 devel
+
 ## scp 1.17.1
 
 - Deprecate `aggregateFeaturesOverAssays`, use
   `QFeatures::aggregateFeatures` instead.
 
-## scp 1.17.0
-
-- New Bioconductor 3.21 devel
+## scp 1.17.2
+
+- Recommend the use of `SummarizedExperiment` instead of
+`SingleCellExperiment` for performance reasons.
+- All functions are now compatible with `SummarizedExperiment`.
+- `data("scp1")` now contains `SummarizedExperiment` objects.
+- By default, `readSCP` and `readSCPfromDIANN` now create
+QFeatures objects that contain `SummarizedExperiment` objects.
+- `readSCP` and `readSCPfromDIANN` have a new parameter:
+`experimentsAsSce` that indicate if the QFeatures should 
+contain `SingleCellExperiment`, default is `FALSE`.
+- `readSCP` and `readSCPfromDIANN` now return a QFeatures of type
+"scp".
+- `scpModelWorkflow` now automatically convert a `SummarizedExperiment`
+to a `SingleCellExperiment`.
 
 # scp 1.16
 

R/ScpModel-Class.R

@@ -9,7 +9,7 @@
 ##' @description
 ##'
 ##' An `ScpModel` object must be always stored in the `metadata()` of
-##' an object that inherits from the `SingleCellExperiment` class. The
+##' an object that inherits from the `SummarizedExperiment` class. The
 ##' `ScpModel` object should **never be accessed directly** by the
 ##' user. Instead, we provide several setter function to retrieve
 ##' information that may be useful to the user.The `ScpModel` class
@@ -18,10 +18,10 @@
 ##' - `scpModelFormula`: a `formula` object controlling which
 ##'   variables are to be modelled.
 ##' - `scpModelInputIndex`: a `numeric(1)`, selecting the assay to use
-##'   in the `SingleCellExperiment` object as input matrix. Note that
+##'   in the `SummarizedExperiment` object as input matrix. Note that
 ##'   this slot serves as a pointer, meaning that the quantitative
 ##'   data is not duplicated. Any change to the assay in the
-##'   `SingleCellExperiment` will impact the estimation of the
+##'   `SummarizedExperiment` will impact the estimation of the
 ##'   `ScpModel` object.
 ##' - `scpModelFilterThreshold`: A `numeric(1)` indicating the minimal
 ##'   n/p ratio required for a feature to be included in further model
@@ -37,7 +37,7 @@
 ##' Each slot has a getter function associated:
 ##'
 ##' - `scpModelNames()`: returns a vector of names of `ScpModel`
-##'   objects stored in the `SingleCellExperiment` object.
+##'   objects stored in the `SummarizedExperiment` object.
 ##' - `scpModelFormula()`: returns the `formula` slot of the `ScpModel`
 ##'   within an object that inherits from the `SummarizedExperiment`
 ##'   class.
@@ -354,7 +354,7 @@ scpModelEffectNames <- function(object, name) {
 ##' @rdname ScpModel-class
 ##'
 ##' @param object An object that inherits from the
-##'     `SingleCellExperiment` class.
+##'     `SummarizedExperiment` class.
 ##'
 ##' @param value An `numeric(1)`, the new value for the n/p ratio
 ##'     threshold

R/ScpModel-ComponentAnalysis.R

@@ -149,7 +149,7 @@ NULL
 ##' @name ScpModel-ComponentAnalysis
 ##'
 ##' @param object An object that inherits from the
-##'     `SingleCellExperiment` class. It must contain an estimated
+##'     `SummarizedExperiment` class. It must contain an estimated
 ##'     `ScpModel` in its metadata.
 ##'
 ##' @param method A `character()` indicating which approach(es) to use
@@ -234,7 +234,7 @@ scpComponentAnalysis <- function(object,
 ##     will use [base::svd()]. If "auto", the function uses "nipals"
 ##     if the data contain missing values and "svd" otherwise.
 ## @param object An object that inherits from the
-##     `SingleCellExperiment` class. It must contain an estimated
+##     `SummarizedExperiment` class. It must contain an estimated
 ##     `ScpModel` in its metadata. Ignored when pcaFun != "auto".
 ## @param name A `character(1)` providing the name to use to retrieve
 ##     the model results. When retrieving a model and `name` is

R/ScpModel-DifferentialAnalysis.R

@@ -102,7 +102,7 @@ NULL
 ##' @name ScpModel-DifferentialAnalysis
 ##'
 ##' @param object An object that inherits from the
-##'     `SingleCellExperiment` class. It must contain an estimated
+##'     `SummarizedExperiment` class. It must contain an estimated
 ##'     `ScpModel` in its metadata.
 ##'
 ##' @param coefficients A `character()` vector with coefficient names

R/ScpModel-Utils.R

@@ -76,7 +76,7 @@ scpAnnotateResults <- function(tableList,
 ##'
 ##' The function uses the data modelling output to generate corrected
 ##' data that can be used for downstream analysis. The input
-##' is expected to be a `SingleCellExperiment` object that contains an
+##' is expected to be a `SummarizedExperiment` object that contains an
 ##' estimated `ScpModel`. There are two approaches:
 ##'
 ##' - `scpKeepEffect()`: keep the effects of interests. The
@@ -95,7 +95,7 @@ scpAnnotateResults <- function(tableList,
 ##' reconstruct the data are the ones that are not removed when
 ##' performing batch correction (see examples).
 ##'
-##' The function returns a new `SingleCellExperiment` that contains an
+##' The function returns a new `SummarizedExperiment` that contains an
 ##' assay with the batch corrected data. Note that the 'ScpModel` is
 ##' erased in this new object.
 ##'
@@ -115,7 +115,7 @@ NULL
 ##' @name ScpModel-DataCorrection
 ##'
 ##' @param object An object that inherits from the
-##'     `SingleCellExperiment` class. It must contain an estimated
+##'     `SummarizedExperiment` class. It must contain an estimated
 ##'     `ScpModel` in its metadata
 ##'
 ##' @param effects A `character()` vector. For `scpKeepEffect()`,
@@ -191,6 +191,8 @@ scpRemoveBatchEffect <- function(object, effects = NULL,
 ##'
 ##' @author Laurent Gatto and Christophe Vanderaa
 ##'
+##' @importFrom methods as
+##' @import SingleCellExperiment
 ##' @export
 ##'
 ##' @examples
@@ -209,11 +211,10 @@ scpRemoveBatchEffect <- function(object, effects = NULL,
 ##' leduc_minimal <- runTSNE(leduc_minimal, dimred = "ASCA_SampleType")
 ##' plotTSNE(leduc_minimal, colour_by = "SampleType")
 addReducedDims <- function(sce, x) {
-    if (!inherits(sce, "SingleCellExperiment"))
-        stop(
-            "'sce' must be a SingleCellExperiment object. Transform ",
-            "your data using 'as(sce, \"SingleCellExperiment\")'."
-        )
+    if (!inherits(sce, "SingleCellExperiment")) {
+        sce <- as(sce, "SingleCellExperiment")
+        message("Convert object to SingleCellExperiment")
+    }
     pcList <- List(lapply(x, .getPCs))
     reducedDims(sce) <- c(reducedDims(sce), pcList)
     sce

R/ScpModel-VarianceAnalysis.R

@@ -65,7 +65,7 @@ NULL
 ##' @name ScpModel-VarianceAnalysis
 ##'
 ##' @param object An object that inherits from the
-##'     `SingleCellExperiment` class. It must contain an estimated
+##'     `SummarizedExperiment` class. It must contain an estimated
 ##'     `ScpModel` in its metadata.
 ##'
 ##' @param name A `character(1)` providing the name to use to retrieve

R/ScpModel-Workflow.R

@@ -14,7 +14,7 @@
 ##' @section Input data:
 ##'
 ##' The main input is `object` that inherits from the
-##' `SingleCellExperiment` class. The quantitative data will be
+##' `SummarizedExperiment` class. The quantitative data will be
 ##' retrieve using `assay(object)`. If `object` contains multiple
 ##' assays, you can specify which assay to take as input thanks to the
 ##' argument `i`, the function will then assume `assay(object, i)` as
@@ -120,7 +120,7 @@ NULL
 ##' @name ScpModel-Workflow
 ##'
 ##' @param object An object that inherits from the
-##'     `SingleCellExperiment` class.
+##'     `SummarizedExperiment` class.
 ##'
 ##' @param formula A `formula` object controlling which variables are
 ##'     to be modelled.
@@ -142,6 +142,10 @@ scpModelWorkflow <- function(object, formula,
                              i = 1,
                              name = "model",
                              verbose = TRUE) {
+    if (!inherits(object, "SingleCellExperiment")) {
+        object <- as(object, "SingleCellExperiment")
+        message("`object` converted to SingleCellExperiment.")
+    }
     if (name %in% names(metadata(object))) {
         warning("An element called '", name, "' is already present ",
                 "in the metadata. The associated content will be ",

R/compute_metrics.R

@@ -48,16 +48,16 @@
     (cumsum(x[order(x)]) / seq_along(x))[order(order(x))]
 }
 
-## @param x A `SingleCellExperiment` object
+## @param x A `SummarizedExperiment` object
 ##     
 ## @param group A `factor()` that indicates how features (rows) should
 ##    be grouped. The CVs are computed for each group separately. 
 ##      
 ## @rdname medianCVperCell
 featureCV <- function(x, group, na.rm = TRUE, norm = "none", nobs = 2, ...) {
     ## Check object
-    if (!inherits(x, "SingleCellExperiment"))
-        stop("'x' must inherit from a 'SingleCellExperiment'")
+    if (!inherits(x, "SummarizedExperiment"))
+        stop("'x' must inherit from a 'SummarizedExperiment'")
     ## Optional normalization(s)   
     if (identical(norm, "SCoPE2")) {
         xnorm <- .normalizeSCP(x, method = "div.median")
@@ -683,14 +683,14 @@ jaccardIndex <- function(object, i, by = NULL) {
 ##'
 ##' ## Simulate data
 ##' ## 1000 features in 100 cells
-##' library(SingleCellExperiment)
+##' library(SummarizedExperiment)
 ##' id <- matrix(FALSE, 1000, 1000)
 ##' id[sample(1:length(id), 5000)] <- TRUE
 ##' dimnames(id) <- list(
 ##'     paste0("feat", 1:1000),
 ##'     paste0("cell", 1:1000)
 ##' )
-##' sce <- SingleCellExperiment(assays = List(id))
+##' sce <- SummarizedExperiment(assays = List(id))
 ##' sim <- QFeatures(experiments = List(id = sce))
 ##' sim$batch <- rep(1:100, each = 10)
 ##' sim$SampleType <- rep(c("A", "B"), each = 500)

R/readSCP.R

@@ -10,8 +10,15 @@
 ##'     [readQFeatures()] or [readQFeaturesFromDIANN()]. See these
 ##'     respective manual pages for details.
 ##'
+##' @param experimentsAsSce A `logical(1)` indicating whether the
+##'     `QFeatures` object should be composed of `SingleCellExperiment`
+##'     objects. By default: `FALSE`, the `QFeatures` object will be composed
+##'     of `SummarizedExperiment` objects. Note that using
+##'     `SingleCellExperiment` can impact the performance.
+##'
 ##' @return An instance of class `SingleCellExperiment` or a
-##'     `QFeatures`, composed of `SingleCellExperiment` objects.
+##'     `QFeatures`, composed of `SingleCellExperiment` or
+##'     `SummarizedExperiment` objects.
 ##'
 ##' @note The `SingleCellExperiment` class is built on top of the
 ##'     `RangedSummarizedExperiment` class. This means that some column names
@@ -67,24 +74,28 @@
 ##' readSCP(assayData = mqScpData,
 ##'         colData = sampleAnnotation,
 ##'         runCol = "Raw.file")
-readSCP <- function(...) {
+readSCP <- function(..., experimentsAsSce = FALSE) {
     ans <- readQFeatures(...)
-    el <- ExperimentList(lapply(experiments(ans),
+    if (experimentsAsSce) {
+        el <- ExperimentList(lapply(experiments(ans),
                                 as, "SingleCellExperiment"))
-    experiments(ans) <- el
-    ans
+        experiments(ans) <- el
+    }
+    setQFeaturesType(ans, "scp")
 }
 
 
 ##' @export
 ##'
 ##' @rdname readSCP
-readSCPfromDIANN <- function(...) {
+readSCPfromDIANN <- function(..., experimentsAsSce = FALSE) {
     ans <- readQFeaturesFromDIANN(...)
-    el <- ExperimentList(lapply(experiments(ans),
+    if (experimentsAsSce) {
+        el <- ExperimentList(lapply(experiments(ans),
                                 as, "SingleCellExperiment"))
-    experiments(ans) <- el
-    ans
+        experiments(ans) <- el
+    }
+    setQFeaturesType(ans, "scp")
 }
 
 ##' @export
@@ -93,6 +104,5 @@ readSCPfromDIANN <- function(...) {
 readSingleCellExperiment <- function(...) {
     ## Read data as SummarizedExperiment
     sce <- readSummarizedExperiment(...)
-    sce <- as(sce, "SingleCellExperiment")
-    return(sce)
+    as(sce, "SingleCellExperiment")
 }

R/transform.R

@@ -1,12 +1,12 @@
 
 ####---- Internal functions ----####
 
-## Internal function that normalizes SingleCellExperiment object using 
+## Internal function that normalizes SummarizedExperiment object using 
 ## proteomics normalization methods available in MsCoreUtils::normalize_matrix
 ##' @importFrom MsCoreUtils normalize_matrix
 .normalizeSCP <- function(x, method, ...) {
-  if(!inherits(x, "SingleCellExperiment")) 
-    stop("The assay must be a 'SingleCellExperiment' object.")
+  if(!inherits(x, "SummarizedExperiment")) 
+    stop("The assay must be a 'SummarizedExperiment' object.")
   e <- normalize_matrix(assay(x), method, ...)
   rownames(e) <- rownames(assay(x))
   colnames(e) <- colnames(assay(x))

README.md

@@ -12,6 +12,7 @@ spectrometry-based single cell proteomics data.  It relies on the
 [`QFeatures`](https://rformassspectrometry.github.io/QFeatures/)
 package to manage and process
 [`SingleCellExperiment`](http://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
+or [`SummarizedExperiment`](http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
 objects.
 
 <img