temp remove liger dep functions

NAMESPACE

@@ -126,7 +126,6 @@ export(Store_Palette_Seurat)
 export(Top_Genes_Factor)
 export(UnRotate_X)
 export(VariableFeaturePlot_scCustom)
-export(Variable_Features_ALL_LIGER)
 export(VlnPlot_scCustom)
 export(plotFactors_scCustom)
 export(scCustomize_Palette)

R/LIGER_Utilities.R

@@ -898,76 +898,76 @@ Plot_By_Meta_LIGER <- function(
 }
 
 
-#' Perform variable gene selection over whole dataset
-#'
-#' Performs variable gene selection for LIGER object across the entire object instead of by
-#' dataset and then taking union.
-#'
-#' @param liger_object LIGER object name.
-#' @param num_genes Number of genes to find. Optimizes the value of `var.thresh`  to get
-#' this number of genes, (Default is NULL).
-#' @param var.thresh Variance threshold. Main threshold used to identify variable genes.
-#' Genes with expression variance greater than threshold (relative to mean) are selected.
-#' (higher threshold -> fewer selected genes).
-#' @param alpha.thresh Alpha threshold. Controls upper bound for expected mean gene
-#' expression (lower threshold -> higher upper bound). (default 0.99)
-#' @param tol Tolerance to use for optimization if num.genes values passed in (default 0.0001).
-#' @param do.plot Display log plot of gene variance vs. gene expression. Selected genes are
-#' plotted in green. (Default FALSE)
-#' @param pt.size Point size for plot.
-#' @param chunk size of chunks in hdf5 file. (Default 1000)
-#'
-#' @return A LIGER Object with variable genes in correct slot.
-#'
-#' @import cli
-#'
-#' @references Matching function parameter text descriptions are taken from `rliger::selectGenes`
-#' which is called by this function after creating new temporary object/dataset.
-#' \url{https://github.com/welch-lab/liger}. (License: GPL-3).
-#'
-#' @export
-#'
-#' @concept liger_object_util
-#'
-#' @examples
-#' \dontrun{
-#' liger_obj <- Variable_Features_ALL_LIGER(liger_object = liger_obj, num_genes = 2000)
-#' }
-#'
-
-Variable_Features_ALL_LIGER <- function(
-  liger_object,
-  num_genes = NULL,
-  var.thresh = 0.3,
-  alpha.thresh = 0.99,
-  tol = 0.0001,
-  do.plot = FALSE,
-  pt.size = 0.3,
-  chunk=1000
-) {
-  Is_LIGER(liger_object = liger_object)
-
-  raw_data <- liger_object@raw.data
-
-  cli_inform(message = "Creating temporary object with combined data.")
-
-  temp_liger <- rliger::createLiger(raw.data = list("dataset" = Merge_Sparse_Data_All(raw_data)), remove.missing = FALSE)
-
-  rm(raw_data)
-  gc()
-
-  cli_inform(message = "Normalizing and identifying variable features.")
-
-  temp_liger <- rliger::normalize(object = temp_liger)
-  temp_liger <- rliger::selectGenes(object = temp_liger, var.thresh = var.thresh, do.plot = do.plot, num.genes = num_genes, tol = tol, alpha.thresh = alpha.thresh, cex.use = pt.size, chunk = chunk)
-  var_genes <- temp_liger@var.genes
-
-  rm(temp_liger)
-  gc()
-
-  liger_object@var.genes <- var_genes
-  return(liger_object)
-}
+# #' Perform variable gene selection over whole dataset
+# #'
+# #' Performs variable gene selection for LIGER object across the entire object instead of by
+# #' dataset and then taking union.
+# #'
+# #' @param liger_object LIGER object name.
+# #' @param num_genes Number of genes to find. Optimizes the value of `var.thresh`  to get
+# #' this number of genes, (Default is NULL).
+# #' @param var.thresh Variance threshold. Main threshold used to identify variable genes.
+# #' Genes with expression variance greater than threshold (relative to mean) are selected.
+# #' (higher threshold -> fewer selected genes).
+# #' @param alpha.thresh Alpha threshold. Controls upper bound for expected mean gene
+# #' expression (lower threshold -> higher upper bound). (default 0.99)
+# #' @param tol Tolerance to use for optimization if num.genes values passed in (default 0.0001).
+# #' @param do.plot Display log plot of gene variance vs. gene expression. Selected genes are
+# #' plotted in green. (Default FALSE)
+# #' @param pt.size Point size for plot.
+# #' @param chunk size of chunks in hdf5 file. (Default 1000)
+# #'
+# #' @return A LIGER Object with variable genes in correct slot.
+# #'
+# #' @import cli
+# #'
+# #' @references Matching function parameter text descriptions are taken from `rliger::selectGenes`
+# #' which is called by this function after creating new temporary object/dataset.
+# #' \url{https://github.com/welch-lab/liger}. (License: GPL-3).
+# #'
+# #' @export
+# #'
+# #' @concept liger_object_util
+# #'
+# #' @examples
+# #' \dontrun{
+# #' liger_obj <- Variable_Features_ALL_LIGER(liger_object = liger_obj, num_genes = 2000)
+# #' }
+# #'
+
+# Variable_Features_ALL_LIGER <- function(
+#   liger_object,
+#   num_genes = NULL,
+#   var.thresh = 0.3,
+#   alpha.thresh = 0.99,
+#   tol = 0.0001,
+#   do.plot = FALSE,
+#   pt.size = 0.3,
+#   chunk=1000
+# ) {
+#   Is_LIGER(liger_object = liger_object)
+#
+#   raw_data <- [email protected]
+#
+#   cli_inform(message = "Creating temporary object with combined data.")
+#
+#   temp_liger <- rliger::createLiger(raw.data = list("dataset" = Merge_Sparse_Data_All(raw_data)), remove.missing = FALSE)
+#
+#   rm(raw_data)
+#   gc()
+#
+#   cli_inform(message = "Normalizing and identifying variable features.")
+#
+#   temp_liger <- rliger::normalize(object = temp_liger)
+#   temp_liger <- rliger::selectGenes(object = temp_liger, var.thresh = var.thresh, do.plot = do.plot, num.genes = num_genes, tol = tol, alpha.thresh = alpha.thresh, cex.use = pt.size, chunk = chunk)
+#   var_genes <- [email protected]
+#
+#   rm(temp_liger)
+#   gc()
+#
+#   [email protected] <- var_genes
+#   return(liger_object)
+# }
 
 
 #' Create a Seurat object containing the data from a liger object