re-roxygenize and devtools::document

DESCRIPTION

@@ -1,9 +1,15 @@
 Package: anglemania
-Title: What the Package Does (One Line, Title Case)
+Title: Feature Extraction for scRNA-seq Dataset Integration
 Version: 0.0.0.9000
-Authors@R: 
-    person("First", "Last", email = "[email protected]", role = c("aut", "cre"))
-Description: What the package does (one paragraph).
+Authors@R: c(
+    person("Aaron", "Kollotzek", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0009-0009-7142-4015")),
+    person("Vedran", "Franke", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-3606-6792")),
+    person("Artem", "Baranovskii", , "[email protected]", role = c("aut", "cre")),
+    person("Altuna", "Akalin", , "[email protected]", role = "ctb")
+  )
+Description: anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It improves conventional usage of highly-variable genes for integration tasks.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -12,12 +18,11 @@ Imports:
     Rcpp,
     Matrix,
     Seurat,
-    data.table,
+    SeuratObject,
+    bigstatsr,
     dplyr,
     magrittr,
-    purrr,
     tidyr,
-    bigstatsr,
     glmGamPoi,
     pbapply
 LinkingTo: 
@@ -28,7 +33,3 @@ Suggests:
     knitr,
     rmarkdown
 VignetteBuilder: knitr
-Config/testthat/edition: 3
-Depends:
-    R (>= 2.10)
-LazyData: true

NAMESPACE

@@ -1,19 +1,50 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
+export("intersect_genes<-")
+export("list_stats<-")
+export("weights<-")
+export(add_unique_batch_key)
+export(batch_key)
 export(big_anglemanise)
 export(big_extract_corr)
 export(big_factorise)
+export(create_anglem)
+export(data_info)
+export(dataset_key)
+export(extract_integration_genes)
 export(get_list_stats)
 export(integrate_by_features)
-import(Seurat)
-importFrom(Matrix,Matrix)
+export(integrate_seurat_list)
+export(intersect_genes)
+export(list_stats)
+export(matrix_list)
+export(select_genes)
+export(weights)
+exportClasses(anglem)
+importFrom(Matrix,rowSums)
+importFrom(Seurat,DefaultAssay)
+importFrom(Seurat,FindIntegrationAnchors)
+importFrom(Seurat,IntegrateData)
+importFrom(Seurat,NormalizeData)
+importFrom(Seurat,RunPCA)
+importFrom(Seurat,RunUMAP)
+importFrom(Seurat,ScaleData)
+importFrom(Seurat,SplitObject)
 importFrom(SeuratObject,LayerData)
 importFrom(bigstatsr,FBM)
-importFrom(bigstatsr,as_FBM)
 importFrom(bigstatsr,big_apply)
+importFrom(bigstatsr,big_cor)
 importFrom(bigstatsr,big_transpose)
+importFrom(bigstatsr,nb_cores)
+importFrom(dplyr,add_count)
+importFrom(dplyr,distinct)
+importFrom(dplyr,group_by)
+importFrom(dplyr,mutate)
+importFrom(dplyr,n_groups)
+importFrom(dplyr,select)
 importFrom(magrittr,"%>%")
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pboptions)
-importFrom(purrr,map)
-useDynLib(anglemania, .registration=TRUE)
+importFrom(tidyr,unite)
+importMethodsFrom(methods,show)

R/big_factorise.R

@@ -43,7 +43,6 @@
 #'   z-score-transformed angle matrix.
 #'
 #' @importFrom bigstatsr FBM big_apply
-#' @importFrom stats set.seed
 #'
 #' @seealso
 #' \code{\link{big_extract_corr}},

R/objects.R

@@ -379,7 +379,6 @@ setMethod("extract_integration_genes", "anglem", function(object) {
 #'   column containing the unique batch key.
 #'
 #' @importFrom tidyr unite
-#' @importFrom SeuratObject "%>%"
 #'
 #' @examples
 #' \dontrun{