update for revision

.Rbuildignore

@@ -12,4 +12,5 @@
 ^\.RData$
 ^\.Ruserdata$
 ^\.Rproj\.user$
-^\.github
+^\.github
+^CITATION\.cff$

CITATION.cff

@@ -0,0 +1,37 @@
+cff-version: 1.2.0
+message: "If you use methylTFRAnnotationMm10, please cite it as below."
+type: software
+title: "methylTFRAnnotationMm10: methylTFR annotations for mm10"
+abstract: >-
+  Precomputed transcription factor binding sites, motif GC frequency tables
+  and a genome-wide GC distribution for the mouse (mm10) genome, for use with the
+  methylTFR package. The data are hosted on AnnotationHub and retrieved on
+  first use.
+authors:
+  - family-names: Gunduz
+    given-names: Irem B.
+    email: irembgunduz@gmail.com
+    orcid: "https://orcid.org/0000-0003-2641-0916"
+version: 0.99.10
+date-released: "2026-09-29"
+doi: 10.18129/B9.bioc.methylTFRAnnotationMm10
+license: Artistic-2.0
+repository-code: "https://github.com/EpigenomeInformatics/methylTFRAnnotationMm10"
+keywords:
+  - R
+  - Bioconductor
+  - AnnotationHub
+  - DNA methylation
+  - transcription factor binding sites
+references:
+  - type: software
+    title: "methylTFR: Quantification of DNA methylation signatures in TFBS"
+    authors:
+      - family-names: Gunduz
+        given-names: Irem B.
+      - family-names: Murugan
+        given-names: Sarath Kumar
+      - family-names: Mueller
+        given-names: Fabian
+    doi: 10.18129/B9.bioc.methylTFR
+    repository-code: "https://github.com/EpigenomeInformatics/methylTFR"

DESCRIPTION

@@ -9,20 +9,25 @@ Description: Precomputed transcription factor binding sites, motif GC
     for sequence composition. The data are hosted on AnnotationHub and
     retrieved on first use; this package provides the accessors and the
     documentation.
-Authors@R: person(
-    given = "Irem B.", family = "Gunduz",
-    email = "irembgunduz@gmail.com", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-2641-0916"))
+Authors@R: c(
+    person("Irem B.", "Gunduz", , "irembgunduz@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-2641-0916")),
+    person("ERA-NET Transcan-Neu III - EPILUNAR", role = "fnd",
+           comment = "Grant 01KT2409"),
+    person("Saarland University", role = "fnd",
+           comment = "NanoBioMed Young Investigator Grant")
+  )
 License: Artistic-2.0
 Encoding: UTF-8
-Version: 0.99.9
+Version: 0.99.10
 Depends: R (>= 4.3.0)
-Imports: AnnotationHub, GenomicRanges, utils
+Imports: AnnotationHub, GenomicRanges, stats
 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
 VignetteBuilder: knitr
 biocViews: AnnotationData, AnnotationHub, FunctionalAnnotation,
-    SequenceAnnotation, Homo_sapiens
+    SequenceAnnotation, Mus_musculus
 BugReports: https://github.com/EpigenomeInformatics/methylTFRAnnotationMm10/issues
 URL: https://github.com/EpigenomeInformatics/methylTFRAnnotationMm10
+Roxygen: list(markdown = FALSE)
 RoxygenNote: 7.3.3
 Config/testthat/edition: 3

NAMESPACE

@@ -1,7 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(availableMotifSets)
 export(getGCfreq)
 export(getGenomeGC)
 export(getTFbindsites)
-import(GenomicRanges)
-importFrom(utils,packageVersion)
+importFrom(GenomicRanges,GRanges)

NEWS.md

@@ -1,10 +1,41 @@
+# methylTFRAnnotationMm10 0.99.10
+
+Changes in response to the Bioconductor review:
+
+* `Authors@R` lists the funders (ERA-NET Transcan-Neu III - EPILUNAR,
+  grant 01KT2409; Saarland University NanoBioMed Young Investigator
+  Grant) with the `fnd` role.
+
+* New package help page `?methylTFRAnnotationMm10` summarising the resources and
+  linking the accessors.
+
+* New help pages describing the structure of each AnnotationHub resource
+  listed in `inst/extdata/metadata.csv`: `?motif_gcfreq`
+  (`?altius_motif_gcfreq`, ...), `?tf_bindsites`
+  (`?altius_tf_bindsites`, ...) and `?genomewide_GC`
+  (`?genomewide_GC_mm10`).
+
+* New exported `availableMotifSets()` listing the accepted motif sets.
+
+* `getGenomeGC()` accepts `"mm10"` (or no argument) and gives an
+  informative error for any other assembly.
+
+* biocViews: `Mus_musculus` instead of `Homo_sapiens`.
+
+* Unit tests now cover the local-directory and AnnotationHub code paths
+  (the hub is mocked, so the tests run offline).
+
+* The vignette no longer hides code: the synthetic example data are
+  built in a visible chunk, every chunk is evaluated, and each accessor's
+  output is printed and explained.
+
 # methylTFRAnnotationMm10 0.99.9
 
 * Initial submission to Bioconductor.
 
 * Provides transcription factor binding sites, motif GC frequency
-  tables and a genome-wide GC distribution for hg38, for the
-  jaspar2020, cisbpv2 and altius motif sets GC frequency tables.
+  tables and a genome-wide GC distribution for mm10, for the
+  jaspar2020, cisbpv2 and altius motif sets.
 
 * Resources are hosted on AnnotationHub and downloaded on first use.
 
@@ -15,4 +46,4 @@
 
 * Fixes on NOTES from biocchecks
 
-* Added 4 spaces as suggested
+* Added 4 spaces as suggested

R/aaa-utils.R

@@ -1,14 +1,33 @@
 .PKG_NAME <- "methylTFRAnnotationMm10"
 .MOTIF_SETS <- c("altius", "cisbpv2", "jaspar2020")
-.ASSEMBLY <- "Mm10"
+.ASSEMBLY <- "mm10"
 
 #' @keywords internal
+#' @noRd
 .local_dir <- function() {
     d <- getOption(
         "methylTFRAnnotationMm10.datadir",
         Sys.getenv("METHYL_TFRANNOTATION_Mm10_DIR", "")
     )
-    if (nzchar(d)) d else NULL
+    if (is.character(d) && length(d) == 1L && nzchar(d)) d else NULL
+}
+
+#' @keywords internal
+#' @noRd
+#' @description AnnotationHub records belonging to this package, as a
+#' character vector of titles named by AnnotationHub ID. Kept separate
+#' from .resolve_resource() so the lookup logic can be unit-tested
+#' without network access.
+.hub_titles <- function() {
+    hub <- AnnotationHub::AnnotationHub()
+    hits <- AnnotationHub::query(hub, .PKG_NAME)
+    stats::setNames(hits$title, names(hits))
+}
+
+#' @keywords internal
+#' @noRd
+.hub_get <- function(id) {
+    AnnotationHub::AnnotationHub()[[id]]
 }
 
 #' @keywords internal
@@ -32,27 +51,40 @@
         }
         return(readRDS(path))
     }
-    hub <- AnnotationHub::AnnotationHub()
-    hits <- AnnotationHub::query(hub, .PKG_NAME)
-    idx <- match(file, hits$title)
+    titles <- .hub_titles()
+    idx <- match(file, titles)
     if (is.na(idx)) {
         stop(
             "Resource not found on AnnotationHub: ", file,
-            "\nAvailable: ", paste(hits$title, collapse = ", ")
+            "\nAvailable: ", paste(titles, collapse = ", ")
         )
     }
-    hits[[names(hits)[idx]]]
+    .hub_get(names(titles)[idx])
 }
 
 #' @keywords internal
 #' @noRd
 .check_motif_set <- function(motifSet) {
-    motifSet <- tolower(motifSet)
-    if (length(motifSet) != 1 || !motifSet %in% .MOTIF_SETS) {
+    if (!is.character(motifSet) || length(motifSet) != 1L ||
+        is.na(motifSet) || !tolower(motifSet) %in% .MOTIF_SETS) {
         stop(
             "Invalid motif set. Available: ",
             paste(.MOTIF_SETS, collapse = ", ")
         )
     }
-    motifSet
+    tolower(motifSet)
+}
+
+#' @title List the motif sets provided by this package
+#' @description Returns the names accepted by the \code{motifSet}
+#' argument of \code{\link{getTFbindsites}} and
+#' \code{\link{getGCfreq}}.
+#' @return A character vector of motif set names.
+#' @seealso \code{\link{methylTFRAnnotationMm10}} for an overview of the
+#' package.
+#' @examples
+#' availableMotifSets()
+#' @export
+availableMotifSets <- function() {
+    .MOTIF_SETS
 }

R/getGCfreq.R

@@ -1,32 +1,40 @@
-#' @title getGCfreq
-#' @description Load the motif GC frequency table for a motif set.
-#' Downloaded from AnnotationHub on first use and cached locally thereafter.
-#' @param motifSet Motif set to load. One of: altius, cisbpv2, jaspar2020,
-#' jaspar2020_distal.
-#' @return A named \code{list} of five-row matrices, one per motif.
-#' @import GenomicRanges
-#' @importFrom utils packageVersion
+#' @title Load motif GC frequency tables
+#' @description Load the motif GC frequency tables for a motif set.
+#' Downloaded from AnnotationHub on first use and cached locally
+#' thereafter.
+#' @details Each table describes the GC composition around one motif's
+#' binding sites. Column \eqn{j} corresponds to the \eqn{j}-th 30 nt
+#' window along the (extended) binding site; row \eqn{i} gives the
+#' fraction of binding sites whose window at that position falls into
+#' genome-wide GC quintile \eqn{i} (row 1 lowest, row 5 highest GC).
+#' Columns therefore sum to one. \pkg{methylTFR} combines these
+#' fractions with the observed methylation per GC bin to obtain the
+#' methylation a motif would be expected to show from sequence
+#' composition alone. See \code{\link{motif_gcfreq}} for the data
+#' format.
+#' @param motifSet Motif set to load. One of
+#' \code{availableMotifSets()}: \code{altius}, \code{cisbpv2},
+#' \code{jaspar2020}. Case-insensitive.
+#' @return A named \code{list} of numeric matrices with five rows (GC
+#' quintiles), one matrix per motif.
+#' @seealso \code{\link{motif_gcfreq}}, \code{\link{getTFbindsites}},
+#' \code{\link{getGenomeGC}}
 #' @examples
-#' # 1. Create a dummy object and save it to a temporary directory
-#' # to bypass AnnotationHub during package checks.
-#' mock_dir <- tempdir()
-#' mock_file <- file.path(mock_dir, "altius_motif_gcfreq.rds")
+#' # Point the package at a temporary directory holding a small mock
+#' # table so the example runs without downloading from AnnotationHub.
+#' mock_dir <- file.path(tempdir(), "gcfreq_example")
+#' dir.create(mock_dir, showWarnings = FALSE)
+#' freq <- matrix(c(0.1, 0.2, 0.4, 0.2, 0.1), nrow = 5, ncol = 3)
+#' saveRDS(list(MA0001.1 = freq), file.path(mock_dir,
+#' "altius_motif_gcfreq.rds"))
+#' old_opt <- options(methylTFRAnnotationMm10.datadir = mock_dir)
 #'
-#' # (Mocking a 5-row matrix as expected by the function output)
-#' mock_data <- list(mock_motif_1 = matrix(0.25, nrow = 5, ncol = 4))
-#' saveRDS(mock_data, mock_file)
-#'
-#' # 2. Temporarily point the package's local directory to tempdir()
-#' old_opt <- getOption("methylTFRAnnotationMm10.datadir")
-#' options(methylTFRAnnotationMm10.datadir = mock_dir)
-#'
-#' # 3. Run the function (it will now read the mock file)
-#' x <- getGCfreq(motifSet = "altius")
-#'
-#' # 4. Restore options and clean up the temporary file
-#' options(methylTFRAnnotationMm10.datadir = old_opt)
-#' file.remove(mock_file)
+#' gcfreqs <- getGCfreq("altius")
+#' gcfreqs$MA0001.1
+#' colSums(gcfreqs$MA0001.1)
 #'
+#' options(old_opt)
+#' unlink(mock_dir, recursive = TRUE)
 #' @export
 getGCfreq <- function(motifSet = "altius") {
     motifSet <- .check_motif_set(motifSet)

R/getGenomeGC.R

@@ -1,36 +1,44 @@
-#' @title getGenomeGC
-#' @description Load the genome-wide GC distribution.
+#' @title Load the genome-wide GC distribution
+#' @description Load the genome-wide GC distribution for mm10.
 #' Downloaded from AnnotationHub on first use and cached locally
 #' thereafter.
-#' @param assembly Genome assembly. Defaults to the assembly this
-#' package was built for.
-#' @return A \code{GRanges} with GC_bias and GC_bin metadata columns.
-#' @import GenomicRanges
-#' @importFrom utils packageVersion
-#' @examples
-#' # 1. Create a dummy object and save it to a temporary directory
-#' mock_dir <- tempdir()
-#' mock_file <- file.path(mock_dir, "genomewide_GC_mm10.rds")
-#'
-#' # Mocking a GRanges object with the expected metadata columns
-#' mock_gr <- GenomicRanges::GRanges("chr1:1-100")
-#' mock_gr$GC_bias <- 0.5
-#' mock_gr$GC_bin <- 1L
-#' saveRDS(mock_gr, mock_file)
+#' @details The genome is tiled into non-overlapping 30 nt windows. Each
+#' window carries its GC fraction and its genome-wide GC quintile.
+#' \pkg{methylTFR} uses the table to assign every methylation call to
+#' a GC bin. See \code{\link{genomewide_GC}} for the data format.
 #'
-#' # 2. Temporarily point the package to tempdir
-#' old_opt <- getOption("methylTFRAnnotationMm10.datadir")
-#' options(methylTFRAnnotationMm10.datadir = mock_dir)
-#'
-#' # 3. Run the function
-#' gc <- getGenomeGC()
+#' The package serves a single assembly, so the argument can be left
+#' out. It is kept so that code written as
+#' \code{getGenomeGC("mm10")} works; any other assembly is an error.
+#' @param assembly Genome assembly. Only \code{"mm10"} (the default)
+#' is available in this package; case-insensitive.
+#' @return A \code{GRanges} with metadata columns \code{GC_bias} (GC
+#' fraction of the window) and \code{GC_bin} (quintile, 1 to 5).
+#' @seealso \code{\link{genomewide_GC}}, \code{\link{getGCfreq}}
+#' @examples
+#' # Point the package at a temporary directory holding a small mock
+#' # object so the example runs without downloading from AnnotationHub.
+#' mock_dir <- file.path(tempdir(), "genomegc_example")
+#' dir.create(mock_dir, showWarnings = FALSE)
+#' gr <- GenomicRanges::GRanges(c("chr1:1-30", "chr1:31-60", "chr1:61-90"))
+#' gr$GC_bias <- c(0.30, 0.43, 0.63)
+#' gr$GC_bin <- c(1L, 3L, 5L)
+#' saveRDS(gr, file.path(mock_dir, "genomewide_GC_mm10.rds"))
+#' old_opt <- options(methylTFRAnnotationMm10.datadir = mock_dir)
 #'
-#' # 4. Restore options and clean up
-#' options(methylTFRAnnotationMm10.datadir = old_opt)
-#' file.remove(mock_file)
+#' getGenomeGC()
 #'
+#' options(old_opt)
+#' unlink(mock_dir, recursive = TRUE)
 #' @export
-getGenomeGC <- function(assembly = .ASSEMBLY) {
-    assembly <- tolower(assembly)
-    .resolve_resource(paste0("genomewide_GC_", assembly, ".rds"))
+getGenomeGC <- function(assembly = "mm10") {
+    if (!is.character(assembly) || length(assembly) != 1L ||
+        is.na(assembly) || tolower(assembly) != .ASSEMBLY) {
+        stop(
+            .PKG_NAME, " provides the GC distribution for ", .ASSEMBLY,
+            " only. Call getGenomeGC() without arguments, or load the ",
+            "methylTFR annotation package for the assembly you need."
+        )
+    }
+    .resolve_resource(paste0("genomewide_GC_", .ASSEMBLY, ".rds"))
 }