Revert "cleanup namespace"

This reverts commit 35d1824.

NAMESPACE

@@ -28,8 +28,8 @@ export(pileup_sites)
 export(raer_example)
 export(read_sparray)
 import(GenomicRanges)
+import(IRanges)
 import(S4Vectors)
-import(SingleCellExperiment)
 import(SummarizedExperiment)
 importFrom(BSgenome,snpsByOverlaps)
 importFrom(BiocFileCache,BiocFileCache)
@@ -59,9 +59,9 @@ importFrom(GenomicAlignments,readGAlignments)
 importFrom(GenomicFeatures,genes)
 importFrom(GenomicFeatures,intronsByTranscript)
 importFrom(GenomicFeatures,mapToTranscripts)
+importFrom(GenomicRanges,GRanges)
 importFrom(IRanges,IRanges)
 importFrom(IRanges,extractList)
-importFrom(IRanges,grouplengths)
 importFrom(IRanges,subsetByOverlaps)
 importFrom(Matrix,colSums)
 importFrom(Matrix,sparseMatrix)
@@ -78,6 +78,7 @@ importFrom(Rsamtools,scanFaIndex)
 importFrom(Rsamtools,seqinfo)
 importFrom(S4Vectors,aggregate)
 importFrom(S4Vectors,unstrsplit)
+importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(data.table,fread)
 importFrom(methods,"slot<-")
 importFrom(methods,as)

R/cache.R

@@ -36,7 +36,7 @@ download_GSE99249 <- function(verbose = TRUE) {
     bfc <- .get_cache()
     fls <- unlist(GSE99249_files)
     fl_paths <- .add_files(fls, paste0(baseURL, fls), bfc, verbose)
-    fl_paths <- utils::relist(fl_paths, GSE99249_files)
+    fl_paths <- relist(fl_paths, GSE99249_files)
     fl_paths
 }
 

R/calc_AEI.R

@@ -59,6 +59,8 @@
 #' @importFrom rtracklayer export
 #' @importFrom Rsamtools scanBamHeader
 #' @importFrom IRanges subsetByOverlaps
+#' @import S4Vectors
+#' @import GenomicRanges
 #'
 #' @export
 calc_AEI <- function(bamfiles,

R/differential_editing.R

@@ -34,6 +34,7 @@
 #' rse <- calc_edit_frequency(rse_adar_ifn)
 #' assay(rse, "edit_freq")[1:5, ]
 #'
+#' @import SummarizedExperiment
 #' @importFrom Matrix colSums
 #' @export
 calc_edit_frequency <- function(rse,
@@ -125,6 +126,7 @@ calc_edit_frequency <- function(rse,
 #' @param min_count OPTIONAL the number of reads used to determine the number of
 #'   edited sites. Default is 10.
 #'
+#' @import SummarizedExperiment
 #' @importFrom Matrix colSums
 #' @noRd
 #' @keywords internal
@@ -167,6 +169,7 @@ count_edits <- function(se, edit_frequency = 0.01, min_count = 10,
 #' @param min_samples The minimum number of samples passing the `min_prop` and
 #'   `max_prop` cutoffs to keep a site.
 #'
+#' @import SummarizedExperiment
 #'
 #' @returns  [RangedSummarizedExperiment] for use with `edgeR` or
 #'  `DESeq2`. Contains a `counts` assay with a matrix formatted

R/pileup.R

@@ -86,6 +86,7 @@
 #'
 #' @importFrom BiocGenerics path
 #' @importFrom Rsamtools index scanFaIndex seqinfo BamFile BamFileList
+#' @importFrom GenomicRanges GRanges
 #' @importFrom IRanges IRanges
 #' @importFrom GenomeInfoDb seqlevels seqinfo seqlengths
 #' @importFrom BiocParallel SerialParam bpstop bplapply
@@ -663,6 +664,8 @@ gr_to_cregions <- function(gr) {
 #'
 #' @return `RangedSummarizedExperiment` populated with assays specified in
 #'   `assay_cols`.
+#' @import GenomicRanges
+#' @import SummarizedExperiment
 #' @importFrom IRanges extractList
 #' @keywords internal
 #' @noRd

R/raer.R

@@ -1,7 +1,6 @@
 #' @docType package
 #' @name raer
-#'
-#' @import SingleCellExperiment SummarizedExperiment GenomicRanges S4Vectors
+
 #' @importFrom utils download.file
 #' @importFrom methods is new as
 #' @importFrom Biostrings vmatchPattern

R/sc-pileup.R

@@ -355,6 +355,7 @@ get_sc_pileup <- function(bamfn, index, id, sites, barcodes,
 #'
 #' @importFrom data.table fread
 #' @importFrom Matrix sparseMatrix
+#' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom R.utils gzip
 #' @export
 read_sparray <- function(mtx_fn, sites_fn, bc_fn,

R/utils.R

@@ -67,7 +67,7 @@ unlist_w_names <- function(x) {
 #' overlapping independent regions found in each chunk (dictated by `n_reads_per_chunk`).
 #' The `A_freq` column indicates the frequency of A bases within the region.
 #'
-#' @importFrom IRanges grouplengths
+#' @import GenomicRanges S4Vectors IRanges
 #' @importFrom Rsamtools ScanBamParam BamFile
 #' @importFrom GenomicAlignments readGAlignments
 #' @examples
@@ -150,6 +150,7 @@ empty_mispriming_record <- function() {
     gr
 }
 
+#' @import GenomicRanges
 merge_pa_peaks <- function(gr) {
     # get 3' end of read
     start(gr[strand(gr) == "+"]) <- end(gr[strand(gr) == "+"])