From 0b16164d4a82c9e247ed61c9a9f1b2c92bbc578e Mon Sep 17 00:00:00 2001
From: cvanderaa <vanderaa.christophe@gmail.com>
Date: Fri, 8 Mar 2024 23:12:32 +0100
Subject: [PATCH] Removed .splitSCE() artefact

---
 R/QFeatures-constructors.R | 52 --------------------------------------
 1 file changed, 52 deletions(-)

diff --git a/R/QFeatures-constructors.R b/R/QFeatures-constructors.R
index 4c3d3098..a37f1cdd 100644
--- a/R/QFeatures-constructors.R
+++ b/R/QFeatures-constructors.R
@@ -578,55 +578,3 @@ readQFeaturesFromDIANN <- function(colData, reportData, extractedData = NULL,
              "the same experiment?")
     extractedData[, cnames]
 }
-
-
-##' Split SingleCellExperiment into an ExperimentList
-##'
-##' The fonction creates an [ExperimentList] containing
-##' [SingleCellExperiment] objects from a [SingleCellExperiment]
-##' object. `f` is used to split `x`` along the rows (`f`` was a feature
-##' variable name) or samples/columns (f was a phenotypic variable
-##' name). If f is passed as a factor, its length will be matched to
-##' nrow(x) or ncol(x) (in that order) to determine if x will be split
-##' along the features (rows) or sample (columns). Hence, the length of
-##' f must match exactly to either dimension.
-##'
-##' This function is not exported. If this is needed, create a pull
-##' request to `rformassspectrometry/QFeatures`.
-##'
-##' @param x a single [SingleCellExperiment] object
-##'
-##' @param f a factor or a character of length 1. In the latter case,
-##'     `f` will be matched to the row and column data variable names
-##'     (in that order). If a match is found, the respective variable
-##'     is extracted, converted to a factor if needed
-##' @noRd
-.splitSCE <- function(x,
-                      f) {
-    ## Check that f is a factor
-    if (is.character(f)) {
-        if (length(f) != 1)
-            stop("'f' must be of lenght one")
-        if (f %in% colnames(rowData(x))) {
-            f <- rowData(x)[, f]
-        }
-        else if (f %in% colnames(colData(x))) {
-            f <- colData(x)[, f]
-        }
-        else {
-            stop("'", f, "' not found in rowData or colData")
-        }
-        if (!is.factor(f))
-            f <- factor(f)
-    }
-    ## Check that the factor matches one of the dimensions
-    if (!length(f) %in% dim(x))
-        stop("length(f) not compatible with dim(x).")
-    if (length(f) == nrow(x)) { ## Split along rows
-        xl <- lapply(split(rownames(x), f = f), function(i) x[i, ])
-    } else { ## Split along columns
-        xl <- lapply(split(colnames(x), f = f), function(i) x[, i])
-    }
-    ## Convert list to an ExperimentList
-    do.call(ExperimentList, xl)
-}